| UMLS-Similarity documentation | Contained in the UMLS-Similarity distribution. |
UMLS::Similarity::ErrorHandler - Provides the error handling of the configuration files for the measures in the UMLS-Similarity package.
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.
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";
}
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.
http://tech.groups.yahoo.com/group/umls-similarity/
http://search.cpan.org/dist/UMLS-Similarity/
Bridget T McInnes <bthomson@cs.umn.edu> Ted Pedersen <tpederse@d.umn.edu>
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.
| UMLS-Similarity documentation | Contained in the UMLS-Similarity distribution. |
# 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__