[Miamexpress-development] scripts/magexpress/BioDataCube ExperimentBioDataCube.pm,NONE,1.1

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Update of /cvsroot/miamexpress/scripts/magexpress/BioDataCube
In directory usw-pr-cvs1:/tmp/cvs-serv3280/BioDataCube

Added Files:
	ExperimentBioDataCube.pm 
Log Message:
say Welcome to some other parts of MIAMExpress into MAGE ;)

--- NEW FILE: ExperimentBioDataCube.pm ---
#!/sw/arch/bin/perl -w

#------------------------------------------------------------------------------
# European Molecular Biology Laboratory
# Eoropean Bioinformatic Institute
# Microarray Informatics
#------------------------------------------------------------------------------
# ExperimentBioDataCube
#
# Path: ../scripts/magexpress/BioDataCube/ExperimentBioDataCube.pm
#
# Description:
# This is ExperimentBioDataCube class which is inherited from 
# Bio::MAGE::BioDataCube class.
#
# Ver   Author         Date      Comments
#------------------------------------------------------------------------------
# 1.0   Mohammad Shoja 23/07/02  Create
#------------------------------------------------------------------------------

package ExperimentBioDataCube;

use strict;
use Class::ObjectTemplate;
use Bio::MAGE::BioAssayData::BioDataCube;

use MX_const;
use lib MX_INC_LIST;

# For interaction with MIAMExpress database
use MX_dbapi1;
use MX_dbapi2;

use MX_init;
use MX_logging;
use magexpress;

use vars qw($VERSION @ISA @EXPORT @EXPORT_OK);

require Exporter;

@ISA = qw(Class::ObjectTemplate Bio::MAGE::BioAssayData::BioDataCube Exporter);

# Items to export into callers namespace by default. Note: do not export
# names by default without a very good reason. Use EXPORT_OK instead.
# Do not simply export all your public functions/methods/constants.
@EXPORT_OK = qw();

#------------------------------------------------------------------------------
# SetAllAssociations
#
# Argument consideration:
# 
# Return value:
# It returns appropriate error code or STATUS_OK.
#
# Ver   Author     Date           Comments
#------------------------------------------------------------------------------
# 1.0   Mohammad   22/04/02       Create
#------------------------------------------------------------------------------
# Description:
# Sets all associations of DerivedBioAssayDescription object, this method actually 
# call all other SetAssociation() methos which are listed below.
#------------------------------------------------------------------------------
sub SetAllAssociations {

    my ($self, $subid) = @_;
    my $rc = STATUS_OK;

    $self->SetAllAssociations_self($subid);

    $self->SetAllAssocoations_ofAssociatedObjects($subid);

    return $rc;
}
#------------------------------------------------------------------------------
# SetAllAssociations_self
#
# Argument consideration:
# 
# submission ID
# (IN)
#
# Return value:
# It returns appropriate error code or STATUS_OK.
#
# Ver   Author     Date           Comments
#------------------------------------------------------------------------------
# 1.0   Mohammad   17/04/02       Create
#------------------------------------------------------------------------------
# Description:
# Sets all associations of DerivedBioAssayDescription object, this method 
# actually call all other SetAssociation() methos which are listed below.
#------------------------------------------------------------------------------
sub SetAllAssociations_self {

    my ($self, $subid) = @_;

    my $rc = STATUS_OK;

    return $rc;
}
#------------------------------------------------------------------------------
# SetAllAssocoations_ofAssociatedObjects
#
# Argument consideration:
# 
# Return value:
# It returns appropriate error code or STATUS_OK.
#
# Ver   Author     Date           Comments
#------------------------------------------------------------------------------
# 1.0   Mohammad   02/05/02       Create
#------------------------------------------------------------------------------
# Description:
# Sets all associations of all associated objects.
#------------------------------------------------------------------------------
sub SetAllAssocoations_ofAssociatedObjects {

    my ($self, $subid) = @_;
    my $rc = STATUS_OK;

    # associations are handled as sub-elements of the current element
    # and we use the association meta-data to instruct how to represent
    # each association
    #
    # We use the IxHash module because the associations are ordered
    # in the same order the DTD expects to receive them, and IxHash
    # preserves insertion order
    tie my %assns_hash, 'Tie::IxHash', $self->associations();

    foreach my $association (keys %assns_hash) {
	my $association_obj;
	{
	    no strict 'refs';
	    my $getter_method = 'get'.ucfirst($association);
	    $association_obj = $self->$getter_method();
	}
	if (defined $association_obj) {

	    my @association_objects;
	    my $cardinality = $assns_hash{$association}->cardinality();
	    if (($cardinality eq CARD_1_TO_N) ||
		($cardinality eq CARD_0_TO_N)) {
		@association_objects = @$association_obj;

	    } else {
		@association_objects = ($association_obj);	
	    }

	    foreach $association_obj (@association_objects) {
		if (defined $association_obj) {
		    $association_obj->SetAllAssociations($subid);
		}
	    }
	}
    }

    return $rc;
}
#------------------------------------------------------------------------------
# LoadData
#
# Argument consideration:
# 
# Return value:
# It returns appropriate error code or STATUS_OK.
#
# Ver   Author     Date           Comments
#------------------------------------------------------------------------------
# 1.0   Mohammad   22/04/02       Create
#------------------------------------------------------------------------------
# Description:
# Load the data from MIAMExpress database into the ExperimentDescription object.
# It returns appropriate error code or STATUS_OK
#------------------------------------------------------------------------------
sub LoadData {

    my ($self, $subid) = @_;
    my $rc = STATUS_OK;

    $self->LoadData_self($subid);

    $self->LoadData_ofAssociatedObjects($subid);

    return $rc;
}
#------------------------------------------------------------------------------
# LoadData_self
#
# Argument consideration:
# 
# Return value:
# It returns appropriate error code or STATUS_OK.
#
# Ver   Author     Date           Comments
#------------------------------------------------------------------------------
# 1.0   Mohammad   23/07/02       Create
#------------------------------------------------------------------------------
# Description:
# Load data of self Object
#------------------------------------------------------------------------------
sub LoadData_self {

    my ($self, $subid) = @_;
    my $rc = STATUS_OK;

    my $exprfnl  = new SX_TEXPRFNL;

    $exprfnl->texprfnl_subid( $subid);

    $rc = MX_DB_GetExperimentFinalData( $subid, $exprfnl);

    if ($rc != STATUS_OK && $rc != REC_NOT_FOUND ) {

	MX_log_err("LoadData_self:",MX_ERR_GEN,__FILE__,__LINE__,
		   "Error in getting experiment final data from database");

	return $rc;
    }

    # Loading the data in object
    $self->setCube($exprfnl->texprfnl_datafile);

    return $rc;
}
#------------------------------------------------------------------------------
# LoadData_ofAssociatedObjects
#
# Argument consideration:
# 
# Return value:
# It returns appropriate error code or STATUS_OK.
#
# Ver   Author     Date           Comments
#------------------------------------------------------------------------------
# 1.0   Mohammad   26/04/02       Create
#------------------------------------------------------------------------------
# Description:
# Load data of all Associated Objects
#------------------------------------------------------------------------------
sub LoadData_ofAssociatedObjects {

    my ($self , $subid) = @_;
    my $rc = STATUS_OK;

    # associations are handled as sub-elements of the current element
    # and we use the association meta-data to instruct how to represent
    # each association
    #
    # We use the IxHash module because the associations are ordered
    # in the same order the DTD expects to receive them, and IxHash
    # preserves insertion order
    tie my %assns_hash, 'Tie::IxHash', $self->associations();

    foreach my $association (keys %assns_hash) {
	my $association_obj;
	{
	    no strict 'refs';
	    $association_obj = $self->$association();
	}
	if (defined $association_obj) {

	    my @association_objects;
	    my $cardinality = $assns_hash{$association}->cardinality();
	    if (($cardinality eq CARD_1_TO_N) ||
		($cardinality eq CARD_0_TO_N)) {
		@association_objects = @$association_obj;

	    } else {
		@association_objects = ($association_obj);	
	    }

	    foreach $association_obj (@association_objects) {
		if (defined $association_obj) {
		    $association_obj->LoadData($subid);
		}
	    }
	}
    }

    return $rc;
}
#------------------------------------------------------------------------------
# ReturnOwnRef
#
# Argument consideration:
# 
# Return value:
# It returns appropriate error code or STATUS_OK.
#
# Ver   Author     Date           Comments
#------------------------------------------------------------------------------
# 1.0   Mohammad   08/05/02       Create
#------------------------------------------------------------------------------
# Description:
# This method create a self object and return its reference
#------------------------------------------------------------------------------
sub ReturnOwnRef {

    return ExperimentBioDataCube->new();

}

# ObjectTemplate automagically creates a new() method for us 
# that method invokes $self->initialize() after first setting all 
# parameters specified in invocation
sub initialize {
    my $self = shift;
}

1;