Import of BTMCINNES/UMLS-Interface-1.25 from CPAN.

gitpan-cpan-distribution: UMLS-Interface gitpan-cpan-version: 1.25 gitpan-cpan-path: BTMCINNES/UMLS-Interface-1.25.tar.gz gitpan-cpan-author: BTMCINNES gitpan-cpan-maturity: released
gitpan · Oct 23, 2014 · 270d288 · 270d288
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diff --git a/CHANGELOG b/CHANGELOG
@@ -1,6 +1,9 @@
 NAME
     UMLS::Interface CHANGES
 
+  Changes from version 1.23 to 1.25
+1. modified the utils/ programs database options - some where 
+   not working correctly. They all should be operational now!
   Changes from version 1.21 to 1.23
     1. added a --relations option to getCuiList.pl in order to obtain the
     number of specified relations from given CUIs

diff --git a/MANIFEST b/MANIFEST
@@ -187,3 +187,4 @@ utils/getSts.pl
 utils/getStString.pl
 utils/getTableNames.pl
 utils/removeConfigData.pl
+META.json                                Module JSON meta-data (added by MakeMaker)
diff --git a/META.json b/META.json
@@ -0,0 +1,45 @@
+{
+   "abstract" : "Perl interface to the Unified Medical Language System (UMLS)",
+   "author" : [
+      "Bridget McInnes <bthomson@cs.umn.edu>, Ted Pedersen <tpederse@d.umn.edu>, Serguei Pakhomov <pakh0002@umn.edu>, Siddharth Patwardhan <sidd@cs.utah.edu>"
+   ],
+   "dynamic_config" : 1,
+   "generated_by" : "ExtUtils::MakeMaker version 6.59, CPAN::Meta::Converter version 2.112150",
+   "license" : [
+      "unknown"
+   ],
+   "meta-spec" : {
+      "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
+      "version" : "2"
+   },
+   "name" : "UMLS-Interface",
+   "no_index" : {
+      "directory" : [
+         "t",
+         "inc"
+      ]
+   },
+   "prereqs" : {
+      "build" : {
+         "requires" : {
+            "ExtUtils::MakeMaker" : 0
+         }
+      },
+      "configure" : {
+         "requires" : {
+            "ExtUtils::MakeMaker" : 0
+         }
+      },
+      "runtime" : {
+         "requires" : {
+            "DBD::mysql" : 0,
+            "DBI" : 0,
+            "Digest::SHA1" : "2.12",
+            "File::Path" : "2.08",
+            "File::Spec" : "3.31"
+         }
+      }
+   },
+   "release_status" : "stable",
+   "version" : "1.25"
+}
diff --git a/META.yml b/META.yml
@@ -1,26 +1,26 @@
---- #YAML:1.0
-name:               UMLS-Interface
-version:            1.23
-abstract:           Perl interface to the Unified Medical Language System (UMLS)
+---
+abstract: 'Perl interface to the Unified Medical Language System (UMLS)'
 author:
-    - Bridget McInnes <bthomson@cs.umn.edu>, Ted Pedersen <tpederse@d.umn.edu>, Serguei Pakhomov <pakh0002@umn.edu>, Siddharth Patwardhan <sidd@cs.utah.edu>
-license:            unknown
-distribution_type:  module
-configure_requires:
-    ExtUtils::MakeMaker:  0
+  - 'Bridget McInnes <bthomson@cs.umn.edu>, Ted Pedersen <tpederse@d.umn.edu>, Serguei Pakhomov <pakh0002@umn.edu>, Siddharth Patwardhan <sidd@cs.utah.edu>'
 build_requires:
-    ExtUtils::MakeMaker:  0
-requires:
-    DBD::mysql:    0
-    DBI:           0
-    Digest::SHA1:  2.12
-    File::Path:    2.08
-    File::Spec:    3.31
-no_index:
-    directory:
-        - t
-        - inc
-generated_by:       ExtUtils::MakeMaker version 6.55_02
+  ExtUtils::MakeMaker: 0
+configure_requires:
+  ExtUtils::MakeMaker: 0
+dynamic_config: 1
+generated_by: 'ExtUtils::MakeMaker version 6.59, CPAN::Meta::Converter version 2.112150'
+license: unknown
 meta-spec:
-    url:      http://module-build.sourceforge.net/META-spec-v1.4.html
-    version:  1.4
+  url: http://module-build.sourceforge.net/META-spec-v1.4.html
+  version: 1.4
+name: UMLS-Interface
+no_index:
+  directory:
+    - t
+    - inc
+requires:
+  DBD::mysql: 0
+  DBI: 0
+  Digest::SHA1: 2.12
+  File::Path: 2.08
+  File::Spec: 3.31
+version: 1.25
diff --git a/lib/UMLS/Interface.pm b/lib/UMLS/Interface.pm
@@ -421,7 +421,7 @@ my $pkg = "UMLS::Interface";
 
 use vars qw($VERSION);
 
-$VERSION = '1.23';
+$VERSION = '1.25';
 
 my $debug = 0;
 

diff --git a/utils/findCuiDepth.pl b/utils/findCuiDepth.pl
@@ -247,13 +247,6 @@ =head1 COPYRIGHT
     exit;
 }
 
-my $database = "umls";
-if(defined $opt_database) { $database = $opt_database; }
-my $hostname = "localhost";
-if(defined $opt_hostname) { $hostname = $opt_hostname; }
-my $socket   = "/tmp/mysql.sock";
-if(defined $opt_socket)   { $socket   = $opt_socket;   }
-
 my $umls = "";
 
 my %option_hash = ();
@@ -283,19 +276,19 @@ =head1 COPYRIGHT
     $option_hash{"username"} = $opt_username;
 }
 if(defined $opt_driver) {
-    $option_hash{"driver"}   = "mysql";
+    $option_hash{"driver"}   = $opt_driver; #"mysql";
 }
 if(defined $opt_database) {
-    $option_hash{"database"} = $database;
+    $option_hash{"database"} = $opt_database;
 }
 if(defined $opt_password) {
     $option_hash{"password"} = $opt_password;
 }
 if(defined $opt_hostname) {
-    $option_hash{"hostname"} = $hostname;
+    $option_hash{"hostname"} = $opt_hostname;
 }
 if(defined $opt_socket) {
-    $option_hash{"socket"}   = $socket;
+    $option_hash{"socket"}   = $opt_socket;
 }
 
 $umls = UMLS::Interface->new(\%option_hash); 
@@ -461,7 +454,7 @@ ()
 #  function to output the version number
 ##############################################################################
 sub showVersion {
-    print '$Id: findCuiDepth.pl,v 1.15 2011/07/12 18:24:29 btmcinnes Exp $';
+    print '$Id: findCuiDepth.pl,v 1.16 2011/08/29 16:37:03 btmcinnes Exp $';
     print "\nCopyright (c) 2008, Ted Pedersen & Bridget McInnes\n";
 }
 

diff --git a/utils/findDFS.pl b/utils/findDFS.pl
@@ -203,16 +203,8 @@ =head1 COPYRIGHT
     exit;
 }
 
-
 my $config = shift;
 
-my $database = "umls";
-if(defined $opt_database) { $database = $opt_database; }
-my $hostname = "localhost";
-if(defined $opt_hostname) { $hostname = $opt_hostname; }
-my $socket   = "/tmp/mysql.sock";
-if(defined $opt_socket)   { $socket   = $opt_socket;   }
-
 my $umls = "";
 
 my %option_hash = ();
@@ -227,19 +219,19 @@ =head1 COPYRIGHT
     $option_hash{"username"} = $opt_username;
 }
 if(defined $opt_driver) {
-    $option_hash{"driver"}   = "mysql";
+    $option_hash{"driver"}   = $opt_driver; 
 }
 if(defined $opt_database) {
-    $option_hash{"database"} = $database;
+    $option_hash{"database"} = $opt_database;
 }
 if(defined $opt_password) {
     $option_hash{"password"} = $opt_password;
 }
 if(defined $opt_hostname) {
-    $option_hash{"hostname"} = $hostname;
+    $option_hash{"hostname"} = $opt_hostname;
 }
 if(defined $opt_socket) {
-    $option_hash{"socket"}   = $socket;
+    $option_hash{"socket"}   = $opt_socket;
 }
 
 $umls = UMLS::Interface->new(\%option_hash); 
@@ -565,7 +557,7 @@ ()
 #  function to output the version number
 ##############################################################################
 sub showVersion {
-    print '$Id: findDFS.pl,v 1.22 2011/04/26 12:19:28 btmcinnes Exp $';
+    print '$Id: findDFS.pl,v 1.23 2011/08/29 16:37:03 btmcinnes Exp $';
     print "\nCopyright (c) 2008, Ted Pedersen & Bridget McInnes\n";
 }
 

diff --git a/utils/findLeastCommonSubsumer.pl b/utils/findLeastCommonSubsumer.pl
@@ -249,13 +249,6 @@ =head1 COPYRIGHT
     push @fileArray, $string;
 }
 
-my $database = "umls";
-if(defined $opt_database) { $database = $opt_database; }
-my $hostname = "localhost";
-if(defined $opt_hostname) { $hostname = $opt_hostname; }
-my $socket   = "/tmp/mysql.sock";
-if(defined $opt_socket)   { $socket   = $opt_socket;   }
-
 my $umls = "";
 
 my $precision   = 4;    
@@ -293,19 +286,19 @@ =head1 COPYRIGHT
     $option_hash{"username"} = $opt_username;
 }
 if(defined $opt_driver) {
-    $option_hash{"driver"}   = "mysql";
+    $option_hash{"driver"}   = $opt_driver;
 }
 if(defined $opt_database) {
-    $option_hash{"database"} = $database;
+    $option_hash{"database"} = $opt_database;
 }
 if(defined $opt_password) {
     $option_hash{"password"} = $opt_password;
 }
 if(defined $opt_hostname) {
-    $option_hash{"hostname"} = $hostname;
+    $option_hash{"hostname"} = $opt_hostname;
 }
 if(defined $opt_socket) {
-    $option_hash{"socket"}   = $socket;
+    $option_hash{"socket"}   = $opt_socket;
 }
 
 
@@ -470,7 +463,7 @@ ()
 #  function to output the version number
 ##############################################################################
 sub showVersion {
-    print '$Id: findLeastCommonSubsumer.pl,v 1.20 2011/04/26 12:19:28 btmcinnes Exp $';
+    print '$Id: findLeastCommonSubsumer.pl,v 1.21 2011/08/29 16:37:03 btmcinnes Exp $';
     print "\nCopyright (c) 2008, Ted Pedersen & Bridget McInnes\n";
 }
 

diff --git a/utils/findNumberOfCloserConcepts.pl b/utils/findNumberOfCloserConcepts.pl
@@ -214,13 +214,6 @@ =head1 COPYRIGHT
     push @fileArray, $string;
 }
 
-my $database = "umls";
-if(defined $opt_database) { $database = $opt_database; }
-my $hostname = "localhost";
-if(defined $opt_hostname) { $hostname = $opt_hostname; }
-my $socket   = "/tmp/mysql.sock";
-if(defined $opt_socket)   { $socket   = $opt_socket;   }
-
 my $umls = "";
 my %option_hash = ();
 
@@ -237,19 +230,19 @@ =head1 COPYRIGHT
     $option_hash{"username"} = $opt_username;
 }
 if(defined $opt_driver) {
-    $option_hash{"driver"}   = "mysql";
+    $option_hash{"driver"}   = $opt_driver;
 }
 if(defined $opt_database) {
-    $option_hash{"database"} = $database;
+    $option_hash{"database"} = $opt_database;
 }
 if(defined $opt_password) {
     $option_hash{"password"} = $opt_password;
 }
 if(defined $opt_hostname) {
-    $option_hash{"hostname"} = $hostname;
+    $option_hash{"hostname"} = $opt_hostname;
 }
 if(defined $opt_socket) {
-    $option_hash{"socket"}   = $socket;
+    $option_hash{"socket"}   = $opt_socket;
 }
 
 $umls = UMLS::Interface->new(\%option_hash); 
@@ -362,7 +355,7 @@ ()
 #  function to output the version number
 ##############################################################################
 sub showVersion {
-    print '$Id: findNumberOfCloserConcepts.pl,v 1.2 2011/04/26 12:19:28 btmcinnes Exp $';
+    print '$Id: findNumberOfCloserConcepts.pl,v 1.3 2011/08/29 16:37:03 btmcinnes Exp $';
     print "\nCopyright (c) 2008, Ted Pedersen & Bridget McInnes\n";
 }
 

diff --git a/utils/findPathToRoot.pl b/utils/findPathToRoot.pl
@@ -230,13 +230,6 @@ =head1 COPYRIGHT
     exit;
 }
 
-my $database = "umls";
-if(defined $opt_database) { $database = $opt_database; }
-my $hostname = "localhost";
-if(defined $opt_hostname) { $hostname = $opt_hostname; }
-my $socket   = "/var/run/mysqld/mysqld.sock";
-if(defined $opt_socket)   { $socket   = $opt_socket;   }
-
 my $umls = "";
 
 my %option_hash = ();
@@ -269,19 +262,19 @@ =head1 COPYRIGHT
     $option_hash{"username"} = $opt_username;
 }
 if(defined $opt_driver) {
-    $option_hash{"driver"}   = "mysql";
+    $option_hash{"driver"}   = $opt_driver;
 }
 if(defined $opt_database) {
-    $option_hash{"database"} = $database;
+    $option_hash{"database"} = $opt_database;
 }
 if(defined $opt_password) {
     $option_hash{"password"} = $opt_password;
 }
 if(defined $opt_hostname) {
-    $option_hash{"hostname"} = $hostname;
+    $option_hash{"hostname"} = $opt_hostname;
 }
 if(defined $opt_socket) {
-    $option_hash{"socket"}   = $socket;
+    $option_hash{"socket"}   = $opt_socket;
 }
 
 $umls = UMLS::Interface->new(\%option_hash); 
@@ -459,7 +452,7 @@ ()
 #  function to output the version number
 ##############################################################################
 sub showVersion {
-    print '$Id: findPathToRoot.pl,v 1.24 2011/05/10 20:59:43 btmcinnes Exp $';
+    print '$Id: findPathToRoot.pl,v 1.25 2011/08/29 16:37:03 btmcinnes Exp $';
     print "\nCopyright (c) 2008, Ted Pedersen & Bridget McInnes\n";
 }