package SBEAMS::Microarray::Settings;

###############################################################################
# Program     : SBEAMS::Microarray::Settings
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id$
#
# Description : This is part of the SBEAMS::Microarray module which handles
#               setting location-dependant variables.
#
###############################################################################


use strict;

#### Begin with the main Settings.pm
use SBEAMS::Connection::Settings qw(:default $LOG_BASE_DIR);
use SBEAMS::Connection::Log;


#### Set up new variables
use vars qw(@ISA @EXPORT 
            $SBEAMS_PART
            $AFFY_DEFAULT_DIR
            @AFFY_DEFAULT_FILES
            $AFFY_ZIP_REQUEST_DIR
            $AFFY_R_CHP_ANALYSIS_PROTOCOL
            $BIOCONDUCTOR_DELIVERY_PATH
            $ADD_ANNOTATION_OUT_FOLDER
            $AFFY_TMP_DIR
            $AFFY_LOG_DIR
);

my $log = SBEAMS::Connection::Log->new();

require Exporter;
@ISA = qw (Exporter);

@EXPORT = qw (
    $SBEAMS_PART 
    $AFFY_TMP_DIR
);

my $affy_file_types = $CONFIG_SETTING{MA_AFFY_DEFAULT_FILES} || '';
@AFFY_DEFAULT_FILES = split ( /\s/, $affy_file_types);

# Convert any relative paths to absolute paths
for my $k qw(MA_LOG_BASE_DIR MA_AFFY_PROBE_DIR MA_BIOC_DELIVERY_PATH
             MA_ANNOTATION_OUT_PATH MA_AFFY_TMP_DIR MA_AFFY_ZIP_REQUEST_DIR
             MA_AFFY_ANNOTATION_PATH ) {
  next unless defined $CONFIG_SETTING{$k};
  if ( $CONFIG_SETTING{$k} !~ /^\// ) {
    my $delim = ($PHYSICAL_BASE_DIR =~ /\/$/) ? '' : '/';
    $CONFIG_SETTING{$k} = $PHYSICAL_BASE_DIR . $delim . $CONFIG_SETTING{$k};
  }
}


#Edit Location to suit installation requirements
$AFFY_LOG_DIR               = $CONFIG_SETTING{MA_LOG_BASE_DIR} || '';
$AFFY_DEFAULT_DIR           = $CONFIG_SETTING{MA_AFFY_PROBE_DIR} || '';
$BIOCONDUCTOR_DELIVERY_PATH = $CONFIG_SETTING{MA_BIOC_DELIVERY_PATH} || '';
$ADD_ANNOTATION_OUT_FOLDER  = $CONFIG_SETTING{MA_ANNOTATION_OUT_PATH} || '';
$AFFY_TMP_DIR               = $CONFIG_SETTING{MA_AFFY_TMP_DIR} || '';
$AFFY_ZIP_REQUEST_DIR       = $CONFIG_SETTING{MA_AFFY_ZIP_REQUEST_DIR} || '';

#Current protocol that describes the R script to produce the CHP like file
$AFFY_R_CHP_ANALYSIS_PROTOCOL = $CONFIG_SETTING{MA_AFFY_R_CHP_PROTOCOL} || '';


#### Override variables from main Settings.pm
$SBEAMS_SUBDIR          = 'Microarray';
$SBEAMS_PART            = 'Microarray';


##############################
### Methods to access data ###
##############################

#+
# get_affy_log_dir
#
#-
sub get_affy_log_dir {
  my $self = shift;

  my $dir = ( $AFFY_LOG_DIR ) ? $AFFY_LOG_DIR :
            ( $LOG_BASE_DIR ) ? $LOG_BASE_DIR :  "$PHYSICAL_BASE_DIR/var/logs";

  if ( !$dir ) {
    $log->warn( 'No logging dir configured' );
  } elsif ( !-e $log ) {
    $log->warn( "Logging dir, $log, does not exist" );
  }

  return $dir;
}

#+
# get_R_exe_path
#
# returns configured path to R executable
#-
sub get_R_exe_path {
  my $self = shift;

  my $rpath = $CONFIG_SETTING{MA_R_EXE_PATH} || '';

  if ( !$rpath ) {
    $log->warn( 'No path to R specified' );
  }

  return $rpath;
}

#+
# get_R_lib_path
#
# returns configured path to R libraries
#-
sub get_R_lib_path {
  my $self = shift;

  my $rlib = $CONFIG_SETTING{MA_R_LIB_PATH} || '';

  if ( !$rlib ) {
    $log->warn( 'No path to R library specified' );
  }

  return $rlib;
}

#+
# get_admin_email
#
# returns configured path to admin_email
#-
sub get_admin_email {
  my $self = shift;

  my $rlib = $CONFIG_SETTING{MA_ADMIN_EMAIL} || '';
  ( $rlib ) = $DBADMIN  =~ /(\w+\@\w+\.\w+)/ unless ( $rlib );

  if ( !$rlib ) {
    $log->warn( 'No Admin email configured! ' );
  }

  return $rlib;
}

#+
# get_batch_system
#
# returns configured batch system, one of fork, sge, pbs
#-
sub get_batch_system {

  return $CONFIG_SETTING{MA_BATCH_SYSTEM} || 'fork';

}

#######################################################
# get_affy_temp_dir_path
# get the path to the top level temp directory
#######################################################
sub get_affy_temp_dir_path {
	my $self = shift;
   
    	return $AFFY_TMP_DIR;
}

#######################################################
# affy_bioconductor_delivery_path
# get the path to the bioconductory delivery folder
#######################################################
sub affy_bioconductor_delivery_path {
	my $self = shift;
   
    	return $BIOCONDUCTOR_DELIVERY_PATH;
}



#######################################################
# get_affy_r_chp_protocol
# get the default affy files extensions need for uploading a complete set of files
#######################################################
sub get_affy_r_chp_protocol {
	my $either = shift;
    
    	my $class = ref($either) || $either;		#class level method no need to get the class name
    	return $AFFY_R_CHP_ANALYSIS_PROTOCOL;
}

#######################################################
# get_AFFY_FILES
# get the default affy files extensions need for uploading a complete set of files
#######################################################
sub get_AFFY_FILES {
				    
    my $either = shift;
    
    my $class = ref($either) || $either;		#class level method no need to get the class name
    return @AFFY_DEFAULT_FILES;
    
}


#######################################################
# set_AFFY_FILES
# Set the default affy files extensions need for uploading a complete set of files.
# Use the default files listed in the define new variables section above if no files are given
# Return the new value(s) set in the @AFFY_DEFAULT_FILES
#######################################################
sub set_AFFY_FILES {
	
	my $either = shift;
	my $files_aref = shift;
	
	 my $class = ref($either) || $either;
	 
	 if ($$files_aref[0] =~ /^\.\w/){
	 	
		@AFFY_DEFAULT_FILES = @{$files_aref};
		print "SET AFFY FILES '@AFFY_DEFAULT_FILES'\n"; 
	}
	return @AFFY_DEFAULT_FILES;
}
	

#######################################################
# get_AFFY_DEFAULT_DIR
# get the default affy data directory 
#######################################################
sub get_AFFY_DEFAULT_DIR {
    my $either = shift;
    
    my $class = ref($either) || $either;
    return $AFFY_DEFAULT_DIR;
    
}

#######################################################
# set_AFFY_DEFAULT_DIR
# Set the path to the affy data dir otherwise use the default listed above in the define new variables section
# Return the value set for $AFFY_DEFAULT_DIR
#######################################################
sub set_AFFY_DEFAULT_DIR {
	
	my $either = shift;
	my $file_path = shift;
	
	 my $class = ref($either) || $either;
	 
	 if (-e $file_path){
	 	
		$AFFY_DEFAULT_DIR = $file_path;
		print "SET AFFY DATA DIR '$AFFY_DEFAULT_DIR'\n"; 
	}
	
	return $AFFY_DEFAULT_DIR;
}

#######################################################
# ZIP_REQUEST_DIR
# get the default to read and write requests to  
#######################################################
sub get_ZIP_REQUEST_DIR {
    my $either = shift;
    
    my $class = ref($either) || $either;
    return $AFFY_ZIP_REQUEST_DIR;
    
}

#######################################################
# set_ZIP_REQUEST_DIR
# Set the path to the affy zip request otherwise use the default listed above in the define new variables section
# Return the value set for $AFFY_DEFAULT_DIR
#######################################################
sub set_ZIP_REQUEST_DIR {
	
	my $either = shift;
	my $file_path = shift;
	
	 my $class = ref($either) || $either;
	 
	 if (-e $file_path){
	 	
		$AFFY_DEFAULT_DIR = $file_path;
		print "SET AFFY ZIP DIR '$AFFY_ZIP_REQUEST_DIR'\n"; 
	}
	
	return $AFFY_ZIP_REQUEST_DIR;
}

#+
# Utility method to return path to affy annotation files.
#-
sub get_affy_annotation_path {
  my $apath = $CONFIG_SETTING{MA_AFFY_ANNOTATION_PATH} || '';
  # Trim trailing spaces
  $apath =~ s/\s+$//g;
  return $apath || "$PHYSICAL_BASE_DIR/var/Microarray/Affy_data/annotation";
}

#######################################################
# get_ANNOTATION_OUT_FOLDER
# get the default folder to hold files generated by the Add_affy_annotation script
#######################################################
sub get_ANNOTATION_OUT_FOLDER {
    my $either = shift;
    
    my $class = ref($either) || $either;
    return $ADD_ANNOTATION_OUT_FOLDER;
    
}
1;