WebService-UMLSKS-Similarity

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bin/ws-getAllowablePath.pl  view on Meta::CPAN

use warnings;
use SOAP::Lite;
use Term::ReadKey;
use WebService::UMLSKS::GetUserData;
use WebService::UMLSKS::ValidateTerm;
use WebService::UMLSKS::Query;
use WebService::UMLSKS::ConnectUMLS;
use WebService::UMLSKS::Similarity;
use WebService::UMLSKS::GetCUIs;
use WebService::UMLSKS::FormGraph;
use Log::Message::Simple qw[msg error debug];

#use get_all_associatedCUIs;
use Getopt::Long;
#use SOAP::Lite +trace => 'debug';
no warnings qw/redefine/;


#Program that returns the shortest path between two concepts using UMLS database.

# Author :			 Mugdha

bin/ws-getAllowablePath.pl  view on Meta::CPAN

# Reference for use of Log package
# http://perldoc.perl.org/Log/Message/Simple.html#msg(%22message-string%22-%5b%2cVERBOSE%5d)


if($log_file ne '' && $verbose eq 1){

open (LOG , '>>', $log_file);


$Log::Message::Simple::MSG_FH     = \*LOG;
$Log::Message::Simple::ERROR_FH   = \*LOG;
$Log::Message::Simple::DEBUG_FH   = \*LOG;

# Following code to print time and date in readable form is taken from following source 
#http://perl.about.com/od/perltutorials/a/perllocaltime_2.htm

my @months = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
my @weekDays = qw(Sun Mon Tue Wed Thu Fri Sat Sun);
my ($second, $minute, $hour, $dayOfMonth, $month, $yearOffset, $dayOfWeek, $dayOfYear, $daylightSavings) = localtime();
my $year = 1900 + $yearOffset;
my $theTime = "$hour:$minute:$second, $weekDays[$dayOfWeek] $months[$month] $dayOfMonth, $year";

lib/WebService/UMLSKS/ConnectUMLS.pm  view on Meta::CPAN

# This module has package Connect which has three subroutines 'new', 'get_pt' and 'connect_umls'.

use warnings;
use SOAP::Lite;
use strict;
no warnings qw/redefine/; #http://www.perlmonks.org/?node_id=582220
package WebService::UMLSKS::ConnectUMLS;

use Log::Message::Simple qw[msg error debug];

# This sub creates a new object of Connect


=head2 new

This sub creates a new object of ConnectUMLS.

=cut

lib/WebService/UMLSKS/FormGraph.pm  view on Meta::CPAN

use WebService::UMLSKS::Query;
use WebService::UMLSKS::ConnectUMLS;
use WebService::UMLSKS::Similarity;
#use Proc::ProcessTable;
#use Graph::Directed;


package WebService::UMLSKS::FormGraph;


use Log::Message::Simple qw[msg error debug];

my %node_cost = ();
my %Graph     = ();
my $counter = 0;
my $const_C = 20;
my $const_k = 1 / 4;
my $absent = 0;

my %MetaCUIs = (
	'C0332280' => 'Linkage concept',

lib/WebService/UMLSKS/GetAllowablePaths.pm  view on Meta::CPAN

#use Proc::ProcessTable;



package WebService::UMLSKS::GetAllowablePaths;

my $pcost = 10;
my $scost = 20;


use Log::Message::Simple qw[msg error debug];
my $verbose = 0;
my $regex = "";

my $current_shortest_length = 150;
my %Concept = ();
my %graph = ();

=head2 new

This sub creates a new object of GetAllowablePaths

lib/WebService/UMLSKS/GetCUIs.pm  view on Meta::CPAN

use SOAP::Lite;
use warnings;
use WebService::UMLSKS::ConnectUMLS;
no warnings qw/redefine/;
use WebService::UMLSKS::Similarity;


package WebService::UMLSKS::GetCUIs;


use Log::Message::Simple qw[msg error debug];

my $got_term = 0;
my $term = "";
my $cui = "";
my %TermCUI = ();

lib/WebService/UMLSKS/GetNeighbors.pm  view on Meta::CPAN

use SOAP::Lite;
use strict;
use warnings;

no warnings qw/redefine/;


package WebService::UMLSKS::GetNeighbors;
our $ConceptInfo_ref;
use Log::Message::Simple qw[msg error debug];
my %ConceptInfo;
my %directions;
my @parents;
my @children;
my @siblings;
my $indentation;
my $verbose = 0;
my @attribute = ();
my @relationattr = ();

lib/WebService/UMLSKS/Query.pm  view on Meta::CPAN

use SOAP::Lite;
use warnings;
use strict;
no warnings qw/redefine/;


package WebService::UMLSKS::Query;


use Log::Message::Simple qw[msg error debug];

=head2 new

This sub creates a new object of Query.

=cut

sub new {
	my $class = shift;
	my $self  = {};

lib/WebService/UMLSKS/Similarity.pm  view on Meta::CPAN

package WebService::UMLSKS::Similarity;

use warnings;
use strict;
use Log::Message::Simple qw[msg error debug];

no warnings qw/redefine/;

=head1 NAME

WebService::UMLSKS::Similarity - access the Unified Medical Language System (UMLS) via Webservices

=head1 VERSION

Version 0.23