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1 =pod
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2
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3 =head1 NAME
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4
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5 Bio::EnsEMBL::Funcgen::RunnableDB::Annotation
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6
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7 =head1 DESCRIPTION
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8
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9 'Annotation' is a base class for runnables running the Annotatin Pipeline
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10 It performs common tasks such as connecting to the EFG DB etc...
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11
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12 =cut
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13
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14 package Bio::EnsEMBL::Funcgen::RunnableDB::Annotation;
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15
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16 use warnings;
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17 use strict;
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18
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19 use Bio::EnsEMBL::Funcgen::Utils::Helper;
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20 use Bio::EnsEMBL::DBSQL::DBConnection;
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21 use Bio::EnsEMBL::DBSQL::DBAdaptor;
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22 use Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor;
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23 use Bio::EnsEMBL::Funcgen::InputSet;
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24 use Bio::EnsEMBL::Funcgen::DataSet;
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25 use Bio::EnsEMBL::Funcgen::FeatureSet;
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26 use Bio::EnsEMBL::Funcgen::AnnotatedFeature;
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27 use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump);
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28 use Data::Dumper;
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29 use DBI;
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30
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31 #use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
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32 use base ('Bio::EnsEMBL::Hive::Process');
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33
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34 #This defines a set of parameters based on given parameters from the pipeline:
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35 sub fetch_input { # nothing to fetch... just the DB parameters...
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36 my $self = shift @_;
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37
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38 my $dnadb_params = $self->param('dnadb') || throw "No parameters for Core DB";
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39 eval{ $self->_dnadba(Bio::EnsEMBL::DBSQL::DBAdaptor->new(%{ $dnadb_params })); };
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40 if($@) { throw "Error creating the Core DB Adaptor: $@"; }
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41 if(!$self->_dnadba()){ throw "Could not connect to Core DB"; }
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42 $self->_dnadb_params($dnadb_params);
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43
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44 #Get efg connection, otherwise fail..
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45 my $efgdb_params = $self->param('efgdb') || throw "No parameters for EFG DB";
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46
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47 eval{
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48 $self->_efgdba(Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(
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49 %{ $efgdb_params },
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50 #Why is this not working???
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51 #-dnadb => $self->_dnadba,
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52 -dnadb_user => $self->_dnadba->dbc->username,
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53 -dnadb_port => $self->_dnadba->dbc->port,
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54 -dnadb_host => $self->_dnadba->dbc->host,
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55 -dnadb_dbname => $self->_dnadba->dbc->dbname,
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56 ));
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57 };
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58
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59 if($@) { throw "Error creating the EFG DB Adaptor: $@"; }
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60 if(!$self->_efgdba()){ throw "Could not connect to EFG DB"; }
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61 $self->_efgdb_params($efgdb_params);
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62
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63 #Get work db connection, otherwise fail..
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64 my $workdb_params = $self->param('workdb') || throw "No parameters for Work server";
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65 $self->_workdb_params($workdb_params);
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66
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67 my $species = $self->param('species') || throw "No species defined";
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68 $self->_species($species);
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69
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70 #Not is use, currently...
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71 #my $release = $self->param('release') || throw "Release number not specified";
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72 #$self->_release($release);
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73
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74 my $work_dir = $self->param('work_dir') || throw "'work_dir' is a required parameter";
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75 $self->_work_dir($work_dir);
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76
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77 #Work with conventions here too?? work_dir/output/dbname ??
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78 my $output_dir = $self->param('output_dir') || throw "'output_dir' is a required parameter";
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79 $self->_output_dir($output_dir);
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80
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81 return 1;
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82 }
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83
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84
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85 sub run {
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86 my $self = shift @_;
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87
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88 return 1;
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89 }
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90
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91
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92 sub write_output {
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93 my $self = shift @_;
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94
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95 return 1;
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96
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97 }
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98
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99
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100 #Private Generic getter and setter
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101 sub _getter_setter {
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102 my ($self, $param_name, $param_value) = @_;
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103 if(!$param_name){ return undef; }
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104 if(!$param_value){
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105 $param_value = $self->param($param_name);
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106 } else {
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107 $self->param($param_name, $param_value);
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108 }
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109 return $param_value;
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110 }
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111
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112 # Private getter / setters : Maybe do some validation in some cases...
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113
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114 #Private getter / setter to the Work DB Connection params
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115 sub _workdb_params {
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116 return $_[0]->_getter_setter('workdb_params',$_[1]);
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117 }
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118
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119 #Private getter / setter to the EFG DB Adaptor
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120 sub _efgdba {
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121 return $_[0]->_getter_setter('efgdb',$_[1]);
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122 }
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123
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124 #Private getter / setter to the EFG DB Connection params
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125 sub _efgdb_params {
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126 return $_[0]->_getter_setter('efgdb_params',$_[1]);
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127 }
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128
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129 #Private getter / setter to the Core DB Adaptor
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130 sub _dnadba {
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131 return $_[0]->_getter_setter('dnadb',$_[1]);
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132 }
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133
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134 #Private getter / setter to the Core DB Connection params
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135 sub _dnadb_params {
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136 return $_[0]->_getter_setter('dnadb_params',$_[1]);
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137 }
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138
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139 #Private getter / setter to the Species name
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140 sub _species {
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141 return $_[0]->_getter_setter('species',$_[1]);
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142 }
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143
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144 #Private getter / setter to the work folder
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145 sub _work_dir {
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146 return $_[0]->_getter_setter('work_dir',$_[1]);
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147 }
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148
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149 #Private getter / setter to the output folder
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150 sub _output_dir {
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151 return $_[0]->_getter_setter('output_dir',$_[1]);
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152 }
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153
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154 #Private getter / setter to the release number
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155 sub _release {
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156 return $_[0]->_getter_setter('release',$_[1]);
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157 }
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158
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159
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160 1;
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