#!/usr/bin/perl
=head1 NAME
getTableNames.pl - This program returns the table names associated
with a specified configuration file or all that have been created
=head1 SYNOPSIS
This program returns the table names associated with a specified
configuration file or all that have been created
=head1 USAGE
Usage: getTableNames.pl [OPTIONS]
=head1 INPUT
=head2 Optional Arguments:
=head3 --config FILE
This is the configuration file. The format of the configuration
file is as follows:
SAB :: <include|exclude> <source1, source2, ... sourceN>
REL :: <include|exclude> <relation1, relation2, ... relationN>
For example, if we wanted to use the MSH vocabulary with only
the RB/RN relations, the configuration file would be:
SAB :: include MSH
REL :: include RB, RN
or
SAB :: include MSH
REL :: exclude PAR, CHD
If you go to the configuration file directory, there will
be example configuration files for the different runs that
you have performed.
=head3 --debug
Sets the debug flag for testing
=head3 --username STRING
Username is required to access the umls database on MySql
unless it was specified in the my.cnf file at installation
=head3 --password STRING
Password is required to access the umls database on MySql
unless it was specified in the my.cnf file at installation
=head3 --hostname STRING
Hostname where mysql is located. DEFAULT: localhost
=head3 --socket STRING
The socket your mysql is using. DEFAULT: /tmp/mysql.sock
=head3 --database STRING
Database contain UMLS DEFAULT: umls
=head4 --help
Displays the quick summary of program options.
=head4 --version
Displays the version information.
=head1 OUTPUT
List of CUIs that are associated with the input term
=head1 SYSTEM REQUIREMENTS
=over
=item * Perl (version 5.8.5 or better) - http://www.perl.org
=back
=head1 AUTHOR
Bridget T. McInnes, University of Minnesota
=head1 COPYRIGHT
Copyright (c) 2007-2009,
Bridget T. McInnes, University of Minnesota
bthomson at cs.umn.edu
Ted Pedersen, University of Minnesota Duluth
tpederse at d.umn.edu
Siddharth Patwardhan, University of Utah, Salt Lake City
sidd@cs.utah.edu
Serguei Pakhomov, University of Minnesota Twin Cities
pakh0002@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.
=cut
###############################################################################
# THE CODE STARTS HERE
###############################################################################
# ================================
# COMMAND LINE OPTIONS AND USAGE
# ================================
use UMLS::Interface;
use Getopt::Long;
eval(GetOptions( "version", "help", "debug", "username=s", "password=s", "hostname=s", "database=s", "socket=s", "config=s")) or die ("Please check the above mentioned option(s).\n");
# if help is defined, print out help
if( defined $opt_help ) {
$opt_help = 1;
&showHelp();
exit;
}
# if version is requested, show version
if( defined $opt_version ) {
$opt_version = 1;
&showVersion();
exit;
}
my $umls = "";
my %option_hash = ();
if(defined $opt_config) {
$option_hash{"config"} = $opt_config;
}
if(defined $opt_debug) {
$option_hash{"debug"} = $opt_debug;
}
if(defined $opt_verbose) {
$option_hash{"verbose"} = $opt_verbose;
}
if(defined $opt_username) {
$option_hash{"username"} = $opt_username;
}
if(defined $opt_driver) {
$option_hash{"driver"} = $opt_driver;
}
if(defined $opt_database) {
$option_hash{"database"} = $opt_database;
}
if(defined $opt_password) {
$option_hash{"password"} = $opt_password;
}
if(defined $opt_hostname) {
$option_hash{"hostname"} = $opt_hostname;
}
if(defined $opt_socket) {
$option_hash{"socket"} = $opt_socket;
}
$umls = UMLS::Interface->new(\%option_hash);
die "Unable to create UMLS::Interface object.\n" if(!$umls);
if(defined $opt_config) {
my $hashRef = $umls->returnTableNames();
my $hashkeys = keys %{$hashRef};
if($hashkeys > 0) {
print "\nThe tables associated with the given configuration file are as follows:\n\n";
print " Table\t\t\t\t\tTable Name\n";
foreach my $name (sort keys %{$hashRef}) {
print " ${$hashRef}{$name}\t$name\n";
}
}
else {
print "There are no tables created for this configuration\n";
}
}
else {
my $database = "umlsinterfaceindex";
my $sdb = "";
if(defined $self->{'username'}) {
$sdb = DBI->connect("DBI:mysql:database=$database;mysql_socket=$socket;host\=$hostname",$username, $password, {RaiseError => 1});
}
else {
my $dsn = "DBI:mysql:$database;mysql_read_default_group=client;";
$sdb = DBI->connect($dsn);
}
print "\nTable\t\t\t\t\t\tTable Name\n";
my $sql = qq{ select TABLENAME, HEX from tableindex};
my $sth = $sdb->prepare( $sql );
$sth->execute();
my($name, $hex);
$sth->bind_columns( undef, \$name, \$hex);
while( $sth->fetch() ) {
print "$hex\t$name\n";
} $sth->finish();
}
##############################################################################
# function to output minimal usage notes
##############################################################################
sub minimalUsageNotes {
print "Usage: getTableNames.pl [OPTIONS]\n\n";
&askHelp();
exit;
}
##############################################################################
# function to output help messages for this program
##############################################################################
sub showHelp() {
print "This is a utility that returns the table names\n";
print "created for a given configuration file\n\n";
print "Usage: getTableNames.pl [OPTIONS] \n\n";
print "Options:\n\n";
print "--config FILE Configuration file\n\n";
print "--debug Sets the debug flag for testing\n\n";
print "--username STRING Username required to access mysql\n\n";
print "--password STRING Password required to access mysql\n\n";
print "--hostname STRING Hostname for mysql (DEFAULT: localhost)\n\n";
print "--database STRING Database contain UMLS (DEFAULT: umls)\n\n";
print "--socket STRING Socket used by mysql (DEFAULT: /tmp.mysql.sock)\n\n";
print "--version Prints the version number\n\n";
print "--help Prints this help message.\n\n";
}
##############################################################################
# function to output the version number
##############################################################################
sub showVersion {
print '$Id: getTableNames.pl,v 1.7 2011/08/29 16:37:03 btmcinnes Exp $';
print "\nCopyright (c) 2008, Ted Pedersen & Bridget McInnes\n";
}
##############################################################################
# function to output "ask for help" message when user's goofed
##############################################################################
sub askHelp {
print STDERR "Type getTableNames.pl --help for help.\n";
}