# UMLS::Similarity::ErrorHandler
# (Last Updated $Id: ErrorHandler.pm,v 1.13 2011/05/18 13:08:08 btmcinnes Exp $)
#
# Perl module that provides a perl interface to the
# Unified Medical Language System (UMLS)
#
# Copyright (c) 2004-2011,
#
# Bridget T. McInnes, University of Minnesota, Twin Cities
# bthomson at cs.umn.edu
#
# Siddharth Patwardhan, University of Utah, Salt Lake City
# sidd at cs.utah.edu
#
# Serguei Pakhomov, University of Minnesota, Twin Cities
# pakh0002 at umn.edu
#
# Ted Pedersen, University of Minnesota, Duluth
# tpederse at d.umn.edu
#
# Ying Liu, University of Minnesota, Twin Cities
# liux0935 at umn.edu
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to
#
# The Free Software Foundation, Inc.,
# 59 Temple Place - Suite 330,
# Boston, MA 02111-1307, USA.
package UMLS::Similarity::ErrorHandler;
use Fcntl;
use strict;
use warnings;
use DBI;
use bytes;
my $e1 = "Measure does not support the configuration option (Error Code 1).";
my $e2 = "Missing configuration option (Error Code 2). ";
my $e3 = "Duplicate configuration option (Error Code 3).";
sub _error {
my $self = shift;
my $measure = shift;
my $string = shift;
my $code = shift;
my $errorstring = "";
if($code == 1) { $errorstring = $e1; }
if($code == 2) { $errorstring = $e2; }
if($code == 3) { $errorstring = $e3; }
print STDERR "ERROR: UMLS::Similarity->$measure\n";
print STDERR "$errorstring\n";
print STDERR "$string\n";
exit;
}
# checks the configuration file for the measure
# input : $measure <- string containing the measure name
# $interface <- UMLS::Interface handler
# output:
sub checkConfig {
my $self = shift;
my $measure = shift;
my $interface = shift;
if($measure=~/(path|cdist|nam|wup|lch|jcn|lin|res)/) {
$self->checkPathBasedMeasures($measure, $interface);
}
elsif($measure=~/(vector|lesk)/ ) {
$self->checkRelatednessMeasures($measure, $interface);
}
}
# check the config file with the path-based and IC measures
# input : $measure <- string containing the measure name
# $interface <- UMLS::Interface handler
sub checkPathBasedMeasures {
my $self = shift;
my $measure = shift;
my $interface = shift;
my $hash = $interface->getConfigParameters();
# set possible options
my %options = ();
$options{"SAB"} = 0;
$options{"REL"} = 0;
$options{"RELA"} = 0;
# get the config options
my $check = 0;
foreach my $param (sort keys %{$hash}) {
$check++;
if(exists $options{$param}) { $options{$param}++; }
else {
my $string = "Option: ($param).\n";
$self->_error($measure, $string, 1);
}
}
# remove the optional parameters
delete $options{"RELA"};
# if the check is zero there are no parameters so
# it is using defaults which is good otherewise
# check to make certain nothing is mising
if($check != 0) {
foreach my $param (sort keys %options) {
if($options{$param} == 0) {
my $string = "Option Missing : $param\n";
$self->_error($measure, $string, 2);
}
if($options{$param} > 1) {
my $string = "Duplicate Options : $param\n";
$self->_error($measure, $string, 3);
}
}
}
}
# check the config file with the relatedness measures
# input : $measure <- string containing the measure name
# $interface <- UMLS::Interface handler
# output:
sub checkRelatednessMeasures {
my $self = shift;
my $measure = shift;
my $interface = shift;
my $hash = $interface->getConfigParameters();
# set possible options
my %options = ();
$options{"SABDEF"} = 0;
$options{"RELDEF"} = 0;
$options{"RELADEF"} = 0;
# get the config options
my $check = 0;
foreach my $param (sort keys %{$hash}) {
$check++;
if(exists $options{$param}) { $options{$param}++; }
else {
my $string = "Option: ($param).\n";
$self->_error($measure, $string, 1);
}
}
# remove the optional parameters
delete $options{"RELADEF"};
# if the check is zero there are no parameters so
# it is using defaults which is good otherewise
# check to make certain nothing is mising
if($check != 0) {
foreach my $param (sort keys %options) {
if($options{$param} == 0) {
my $string = "Option Missing : $param\n";
$self->_error($measure, $string, 2);
}
if($options{$param} > 1) {
my $string = "Duplicate Options : $param\n";
$self->_error($measure, $string, 3);
}
}
}
}
# sets up the error handler module
# input : $measure <- string containing the measure name
# $interface <- UMLS::Interface handler
# output: $self
sub new {
my $self = {};
my $className = shift;
my $measure = shift;
my $interface = shift;
# Bless the object.
bless($self, $className);
# check the config options
$self->checkConfig($measure, $interface);
return $self;
}
1;
__END__
=head1 NAME
UMLS::Similarity::ErrorHandler - Provides the error
handling of the configuration files for the measures
in the UMLS-Similarity package.
=head1 DESCRIPTION
This package provides the error handeling of the configuration
files for the measures in the UMLS-Similarity package.
For more information please see the UMLS::Similarity.pm
documentation.
=head1 SYNOPSIS
use UMLS::Interface;
use UMLS::Similarity::ErrorHandler;
my $umls = UMLS::Interface->new();
die "Unable to create UMLS::Interface object.\n" if(!$umls);
$errorhandler = UMLS::Similarity::ErrorHandler->new("lch", $umls);
if(! defined $errorhandler) {
print STDERR "The error handler did not get loaded properly.\n";
exit;
}
else {
print "This checks that the interface is set up for the measure. ";
print "All looks good.\n\n";
}
=head1 INSTALL
To install the module, run the following magic commands:
perl Makefile.PL
make
make test
make install
This will install the module in the standard location. You will, most
probably, require root privileges to install in standard system
directories. To install in a non-standard directory, specify a prefix
during the 'perl Makefile.PL' stage as:
perl Makefile.PL PREFIX=/home/sid
It is possible to modify other parameters during installation. The
details of these can be found in the ExtUtils::MakeMaker
documentation. However, it is highly recommended not messing around
with other parameters, unless you know what you're doing.
=head1 SEE ALSO
http://tech.groups.yahoo.com/group/umls-similarity/
http://search.cpan.org/dist/UMLS-Similarity/
=head1 AUTHOR
Bridget T McInnes <bthomson@cs.umn.edu>
Ted Pedersen <tpederse@d.umn.edu>
=head1 COPYRIGHT
Copyright (c) 2010-2011
Bridget T. McInnes, University of Minnesota
bthomson at umn.edu
Ted Pedersen, University of Minnesota Duluth
tpederse at d.umn.edu
Siddharth Patwardhan, University of Utah, Salt Lake City
sidd at cs.utah.edu
Serguei Pakhomov, University of Minnesota Twin Cities
pakh0002 at umn.edu
Ying Liu, University of Minnesota Twin Cities
liux0395 at umn.edu
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program; if not, write to
The Free Software Foundation, Inc.,
59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.