diff variant_effect_predictor/Bio/EnsEMBL/DBLoader.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/DBLoader.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,131 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBLoader - Run time database loader
+
+=head1 SYNOPSIS
+
+    $db =
+      Bio::EnsEMBL::DBLoader->new( "Bio::EnsEMBL::DBSQL::DBAdaptor/"
+        . "host=localhost;"
+        . "dbname=homo_sapiens_core_19_34a;"
+        . "user=ensro;" );
+
+    # $db is a database object
+    $db = Bio::EnsEMBL::DBLoader->standard();
+
+    # equivalent to
+    # Bio::EnsEMBL::DBLoader->new( $ENV{'ENSEMBL_DATABASE'} );
+
+=head1 DESCRIPTION
+
+This system provides a run-time loading of the database for ensembl,
+allowing two things
+
+    a) Only "using" the database module which is required for a
+       particular implementation
+
+    b) Providing a simple string method to indicate where the database
+       is, allowing per sites defaults and other things as such
+
+
+The string is parsed as follows:
+
+Before the / is the Perl database object to load, after are the
+parameters to pass to that database.  The parameters are series of
+key=values separated by semi-colons.  These are passed as a hash to the
+new method of the database object
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::DBLoader;
+
+use strict;
+
+
+=head2 new
+
+  Arg [1]    : string $string
+               An Ensembl database locator string.
+  Example    : Bio::EnsEMBL::DBSQL::DBLoader->new("Bio::EnsEMBL::DBSQL::DBAdaptor/host=localhost;dbname=homo_sapiens_core_19_34a;user=ensro;"
+  Description: Connects to an Ensembl database using the module specified in
+               the locator string.
+  Returntype : The module specified in the load string is returned.
+  Exceptions : thrown if the specified module cannot be instantiated or the
+               locator string cannot be parsed
+  Caller     : ?
+  Status     : Stable
+
+=cut
+
+sub new{
+   my ($class,$string) = @_;
+   my ($module,%hash);
+
+   $string =~ /(\S+?)\/([\S+\s*]+)/ || die "Could not parse [$string] as a ensembl database locator. Needs database_module/params";
+   $module = $1;
+   my $param = $2;
+
+   &_load_module($module);
+   my @param = split(/;/,$param);
+   foreach my $keyvalue ( @param ) {
+       $keyvalue =~ /(\S+?)=([\S*\s*]*)/ || do { warn("In loading $keyvalue, could not split into keyvalue for loading $module. Ignoring"); next; };
+
+       my $key = $1;
+       my $value = $2;
+
+       $hash{"-$key"} = $value;
+   }
+   
+   my @kv = %hash;
+
+   return "$module"->new(%hash);
+}
+
+
+sub _load_module{
+  my ($modulein) = @_;
+  my ($module,$load,$m);
+
+  $module = "_<$modulein.pm";
+  $load = "$modulein.pm";
+  $load =~ s/::/\//g;
+  
+  return 1 if $main::{$module};
+  eval {
+    require $load;
+  };
+  if( $@ ) {
+    print STDERR <<END;
+$load: cannot be found
+Exception $@
+
+END
+  ;
+    return;
+  }
+  return 1;
+}
+
+1;