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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::DBLoader - Run time database loader
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24
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25 =head1 SYNOPSIS
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26
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27 $db =
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28 Bio::EnsEMBL::DBLoader->new( "Bio::EnsEMBL::DBSQL::DBAdaptor/"
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29 . "host=localhost;"
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30 . "dbname=homo_sapiens_core_19_34a;"
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31 . "user=ensro;" );
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32
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33 # $db is a database object
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34 $db = Bio::EnsEMBL::DBLoader->standard();
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35
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36 # equivalent to
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37 # Bio::EnsEMBL::DBLoader->new( $ENV{'ENSEMBL_DATABASE'} );
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38
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39 =head1 DESCRIPTION
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40
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41 This system provides a run-time loading of the database for ensembl,
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42 allowing two things
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43
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44 a) Only "using" the database module which is required for a
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45 particular implementation
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46
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47 b) Providing a simple string method to indicate where the database
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48 is, allowing per sites defaults and other things as such
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49
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50
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51 The string is parsed as follows:
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52
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53 Before the / is the Perl database object to load, after are the
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54 parameters to pass to that database. The parameters are series of
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55 key=values separated by semi-colons. These are passed as a hash to the
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56 new method of the database object
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57
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58 =head1 METHODS
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59
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60 =cut
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61
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62 package Bio::EnsEMBL::DBLoader;
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63
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64 use strict;
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65
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66
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67 =head2 new
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68
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69 Arg [1] : string $string
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70 An Ensembl database locator string.
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71 Example : Bio::EnsEMBL::DBSQL::DBLoader->new("Bio::EnsEMBL::DBSQL::DBAdaptor/host=localhost;dbname=homo_sapiens_core_19_34a;user=ensro;"
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72 Description: Connects to an Ensembl database using the module specified in
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73 the locator string.
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74 Returntype : The module specified in the load string is returned.
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75 Exceptions : thrown if the specified module cannot be instantiated or the
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76 locator string cannot be parsed
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77 Caller : ?
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78 Status : Stable
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79
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80 =cut
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81
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82 sub new{
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83 my ($class,$string) = @_;
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84 my ($module,%hash);
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85
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86 $string =~ /(\S+?)\/([\S+\s*]+)/ || die "Could not parse [$string] as a ensembl database locator. Needs database_module/params";
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87 $module = $1;
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88 my $param = $2;
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89
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90 &_load_module($module);
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91 my @param = split(/;/,$param);
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92 foreach my $keyvalue ( @param ) {
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93 $keyvalue =~ /(\S+?)=([\S*\s*]*)/ || do { warn("In loading $keyvalue, could not split into keyvalue for loading $module. Ignoring"); next; };
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94
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95 my $key = $1;
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96 my $value = $2;
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97
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98 $hash{"-$key"} = $value;
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99 }
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100
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101 my @kv = %hash;
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102
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103 return "$module"->new(%hash);
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104 }
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105
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106
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107 sub _load_module{
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108 my ($modulein) = @_;
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109 my ($module,$load,$m);
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110
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111 $module = "_<$modulein.pm";
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112 $load = "$modulein.pm";
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113 $load =~ s/::/\//g;
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114
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115 return 1 if $main::{$module};
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116 eval {
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117 require $load;
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118 };
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119 if( $@ ) {
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120 print STDERR <<END;
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121 $load: cannot be found
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122 Exception $@
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123
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124 END
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125 ;
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126 return;
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127 }
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128 return 1;
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129 }
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130
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131 1;
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