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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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1 package CPT::OutputFiles;
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2 use Carp;
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3 use Moose;
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4 use strict;
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5 use warnings;
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6 use autodie;
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7 use File::Spec;
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8
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10 # ABSTRACT: Handles script outputs in a sane way, providing facilities to format data and name files for regular use, or in galaxy.
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11
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12
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13 # A list of acceptable ouput formats. Some/many of these may be missing implementations.
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14 # For instance, the pandoc output format is completely unimplemented
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15 # These will NEED to be re-worked.
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16 has 'acceptable_formats' => (
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17 is => 'ro',
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18 isa => 'HashRef',
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19 default => sub {
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20 {
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21 'text/tabular' => [qw(TSV TSV_U CSV CSV_U XLS ODS Dumper JSON YAML XLSX)],
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22 'genomic/annotated' => [qw(ABI Ace AGAVE ALF AsciiTree BSML BSML_SAX ChadoXML Chaos ChaosXML CTF EMBL EntrezGene Excel Exp Fasta Fastq GAME GCG Genbank Interpro KEGG LargeFasta LaserGene LocusLink PHD PIR PLN Qual Raw SCF SeqXML Strider Swiss Tab TIGR TIGRXML TinySeq ZTR)],
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23 'genomic/raw' => [qw(Fasta)],
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24 'genomic/interval' => [qw(GFF3)],
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25 'text/html' => [qw(HTML)], # Theoretically this will be consumed by text/report
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26 'text/report' => [qw(Pandoc)],
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27 'text/plain' => [qw(TXT CONF)],
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28 'image/svg' => [qw(SVG)],
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29 'image/png' => [qw(PNG)],
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30 'archive' => [qw(tar.gz zip tar)],
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31 'Dummy' => [qw(Dummy)],
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32 }
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33 }
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34 );
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35
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36 has 'format_mapping' => (
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37 is => 'ro',
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38 isa => 'HashRef',
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39 default => sub {
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40 {
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41 'TSV' => 'tabular',
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42 'CSV' => 'tabular',
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43 'TSV_U' => 'tabular',
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44 'CSV_U' => 'tabular',
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45 'XLS' => 'data',
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46 'ODS' => 'data',
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47 'Dumper' => 'txt',
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48 'JSON' => 'txt',
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49 'YAML' => 'txt',
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50 'XLSX' => 'data',
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51 'Fasta' => 'fasta',
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52 'GFF3' => 'interval',
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53 'HTML' => 'html',
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54 'Pandoc' => 'txt',
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55 'TXT' => 'txt',
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56 'CONF' => 'txt',
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57 'SVG' => 'xml',
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58 'PNG' => 'png',
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59 'Dummy' => 'data',
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60 'tar.gz' => 'tar.gz',
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61 'zip' => 'zip',
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62 'tar' => 'tar',
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63 #Genomic formats
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64 'ABI' => 'data',
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65 'Ace' => 'txt',
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66 'AGAVE' => 'xml',
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67 'ALF' => '',
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68 'AsciiTree' => 'txt',
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69 'BSML' => 'xml',
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70 'BSML_SAX' => 'xml',
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71 'ChadoXML' => 'xml',
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72 'Chaos' => 'xml',
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73 'ChaosXML' => 'xml',
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74 'CTF' => 'data',
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75 'EMBL' => 'txt',
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76 'EntrezGene' => 'txt',
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77 'Excel' => 'data',
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78 'Exp' => 'txt',
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79 'Fastq' => 'fastq',
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80 'GAME' => 'xml',
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81 'GCG' => 'txt',
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82 'Genbank' => 'txt',
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83 'Interpro' => 'xml',
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84 'KEGG' => 'txt',
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85 'LargeFasta' => 'txt',
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86 'LaserGene' => 'data',
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87 'LocusLink' => 'data',
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88 'PHD' => 'data',
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89 'PIR' => 'data',
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90 'PLN' => 'data',
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91 'Qual' => 'data',
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92 'Raw' => 'txt',
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93 'SCF' => 'data',
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94 'SeqXML' => 'xml',
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95 'Strider' => 'data',
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96 'Swiss' => 'txt',
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97 'Tab' => 'tabular',
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98 'TIGR' => 'xml',
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99 'TIGRXML' => 'xml',
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100 'TinySeq' => 'xml',
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101 'ZTR' => 'data',
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102 }
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103 }
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104 );
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105
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106 sub valid_formats {
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107 my ($self, $format) = @_;
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108 return ${$self->acceptable_formats()}{$format};
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109 }
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110
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111 sub get_format_mapping{
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112 my ($self, $format) = @_;
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113 return ${$self->format_mapping()}{$format};
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114 }
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115
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116
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117 # User supplied options
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118 has 'name' => ( is => 'ro', isa => 'Str' );
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119 has 'GGO' => ( is => 'ro', isa => 'Any' );
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120 has 'galaxy' => (is => 'rw', isa => 'Bool');
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121
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122 # These are extracted on init from from CPT
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123 has 'output_id' => (is => 'rw', isa => 'Str');
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124 has 'output_label' => (is => 'rw', isa => 'Str');
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125 has 'output_opts' => (is => 'rw', isa => 'HashRef');
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126 # From galaxy
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127 has 'new_file_path' => (is => 'rw', isa => 'Str');
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128 has 'files_path' => (is => 'rw', isa => 'Str');
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129 has 'files_id' => (is => 'rw', isa => 'Str');
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130 # ???
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131 has 'parent_filename' => (is => 'rw', isa => 'Str');
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132 has 'parent_internal_format' => (is => 'rw', isa => 'Str');
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133 has 'parent_default_output_format' => (is => 'rw', isa => 'Str');
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134
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135 has 'init_called' => (is => 'rw', isa =>'Bool');
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136
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137 sub initFromArgs {
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138 my ($self, %args) = @_;
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139
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140 # We will only ever care about one (as there is one of these objects
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141 # per registered output)
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142 my %registered_outputs = %{$self->GGO()->registered_outputs()};
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143 # If the output name specified in "name" was not known to registered_outputs
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144 if(!defined($self->name())){
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145 croak("You must supply a name to the instantiation of CRR");
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146 }
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147 #if(!defined($registered_outputs{$args{name}})){
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148 #croak("The script author tried to call GGO's classyReturnResults method with an output file not mentioned in the outputs section.");
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149 #}
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150
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151 # Carrying on
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152 # We grab the pre-specified data regarding that output
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153 my %reg_out_params = %{$registered_outputs{$self->name()}};
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154 # Store these for future calls of sub/var
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155 $self->output_id($self->name());
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156 $self->output_label($reg_out_params{description});
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157 $self->output_opts($reg_out_params{options});
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158
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159
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160 $self->parent_internal_format($reg_out_params{options}{data_format});
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161 $self->parent_default_output_format($reg_out_params{options}{default_format});
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162 $self->parent_filename($reg_out_params{options}{default});
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163
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164 # Special variables
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165 # --genemark "${genemark}" --genemark_format "${genemark_format}"
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166 # --genemark_files_path "${genemark_files_path}"
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167 # --genemark_id "${genemark_id}"
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168
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169 # If they've specified a filename on the command line, that should
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170 # override the default value
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171 if(defined $self->GGO->opt->{$self->name()}){
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172 $self->parent_filename($self->GGO->opt->{$self->name()});
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173 }
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174 # If they've specified a {str}_format option on the command line, that
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175 # should override the default value
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176 if(defined $self->GGO->opt->{$self->name() . '_format'}){
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177 $self->parent_default_output_format($self->GGO->opt->{$self->name() . '_format'});
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178 }
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179
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180 # Grab supporting files path (added as new history items)
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181 $self->new_file_path($self->GGO->opt->{outfile_supporting});
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182 # Copy galaxy specific variables
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183 if(defined $self->GGO->opt->{$self->name() . '_files_path'}){
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184 $self->files_path($self->GGO->opt->{$self->name() . '_files_path'});
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185 }
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186 if(defined $self->GGO->opt->{$self->name() . '_id'}){
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187 $self->files_id($self->GGO->opt->{$self->name() . '_id'});
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188 }
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189
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190 # If --galaxy has been specified, we need to be aware of this
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191 if ( $self->GGO->opt->{galaxy} ) {
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192 $self->galaxy(1);
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193 }else{
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194 $self->galaxy(0);
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195 }
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196 $self->init_called(1);
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197 }
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198
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199
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200
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201 has 'times_called' => ( is => 'rw', isa => 'Num', default => sub {0} );
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202 has 'naming_strategy' => ( is => 'rw', isa => 'Str', default => "norm" ); #Other options are "var" and "sub"
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203
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204
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205 sub _genCRR {
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206 my ($self, %args) = @_;
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207 if(!$self->init_called()){
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208 $self->initFromArgs(%args);
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209 }
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210
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211 # If the user supplied a custom extension, pull that (useful in
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212 # dummy/data output type)
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213 if(defined $args{extension}){
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214 $self->extension($args{extension});
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215 }
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216
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217 # This is a mandatory parameter
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218 if(!defined $args{filename}){
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219 $self->given_filename($self->parent_filename());
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220 }else{
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221 $self->given_filename($args{filename});
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222 }
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223
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224 # Allow overriding default format parameters
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225 my $writer = $self->writer_for_format(
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226 defined $args{data_format} ? $args{data_format} : $self->parent_internal_format(),
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227 defined $args{format_as} ? $args{format_as} : $self->parent_default_output_format(),
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228 );
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229
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230 # Ugh
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231 $writer->OutputFilesClass($self);
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232 if($args{'data'}){
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diff changeset
233 $writer->data( $args{'data'} );
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parents:
diff changeset
234 }
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cpt
parents:
diff changeset
235 $writer->process_data();
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cpt
parents:
diff changeset
236 $writer->write();
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cpt
parents:
diff changeset
237 my @returned_filenames = @{$writer->used_filenames()};
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parents:
diff changeset
238 print STDERR join("\n",map{"FN: $_"} @returned_filenames)."\n";
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cpt
parents:
diff changeset
239 $self->bump_times_called();
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cpt
parents:
diff changeset
240 return @returned_filenames;
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parents:
diff changeset
241 }
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parents:
diff changeset
242
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cpt
parents:
diff changeset
243
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cpt
parents:
diff changeset
244 sub CRR {
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cpt
parents:
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245 my ( $self, %args ) = @_;
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cpt
parents:
diff changeset
246 return $self->_genCRR(%args);
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cpt
parents:
diff changeset
247 }
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parents:
diff changeset
248
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cpt
parents:
diff changeset
249
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parents:
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250 sub subCRR {
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cpt
parents:
diff changeset
251 my ( $self, %args ) = @_;
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cpt
parents:
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252 # Change naming behaviour
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cpt
parents:
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253 $self->naming_strategy('sub');
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cpt
parents:
diff changeset
254 return $self->_genCRR(%args);
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cpt
parents:
diff changeset
255 }
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cpt
parents:
diff changeset
256
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cpt
parents:
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257
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cpt
parents:
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258 sub varCRR {
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cpt
parents:
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259 my ( $self, %args ) = @_;
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cpt
parents:
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260 # Change naming behaviour
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cpt
parents:
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261 $self->naming_strategy('var');
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cpt
parents:
diff changeset
262 return $self->_genCRR(%args);
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cpt
parents:
diff changeset
263 }
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cpt
parents:
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264
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cpt
parents:
diff changeset
265
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parents:
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266 sub bump_times_called{
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cpt
parents:
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267 my ($self) = @_;
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cpt
parents:
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268 $self->times_called($self->times_called() + 1 );
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cpt
parents:
diff changeset
269 return $self->times_called();
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parents:
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270 }
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parents:
diff changeset
271
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cpt
parents:
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272
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parents:
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273 sub writer_for_format{
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cpt
parents:
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274 my($self, $format, $requested) = @_;
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cpt
parents:
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275
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parents:
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276 # For the specified data_format, grab the acceptable handlers for that format
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parents:
diff changeset
277 my %acceptable = %{$self->acceptable_formats()};
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cpt
parents:
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278 my %acceptable_handlers = map { $_ => 1 } @{ $acceptable{ $format } };
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cpt
parents:
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279
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cpt
parents:
diff changeset
280 if (!$acceptable_handlers{$requested} ) {
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cpt
parents:
diff changeset
281 carp(sprintf( "Unacceptable output format choice [%s] for internal"
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cpt
parents:
diff changeset
282 ."data type for type %s. Acceptable formats are [%s]."
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cpt
parents:
diff changeset
283 ."Alternatively, unacceptable output file.", $requested, $format,
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cpt
parents:
diff changeset
284 join( ', ', keys(%acceptable_handlers) ) ));
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cpt
parents:
diff changeset
285 }
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cpt
parents:
diff changeset
286
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cpt
parents:
diff changeset
287 if ( $requested eq 'Dumper' ) {
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cpt
parents:
diff changeset
288 require CPT::Writer::Dumper;
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cpt
parents:
diff changeset
289 return CPT::Writer::Dumper->new();
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parents:
diff changeset
290 }
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cpt
parents:
diff changeset
291 elsif ( $requested eq 'TSV' ) {
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cpt
parents:
diff changeset
292 require CPT::Writer::TSV;
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cpt
parents:
diff changeset
293 return CPT::Writer::TSV->new();
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parents:
diff changeset
294 }
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parents:
diff changeset
295 elsif ( $requested eq 'CSV' ) {
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cpt
parents:
diff changeset
296 require CPT::Writer::CSV;
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cpt
parents:
diff changeset
297 return CPT::Writer::CSV->new();
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cpt
parents:
diff changeset
298 }
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cpt
parents:
diff changeset
299 elsif ( $requested eq 'TSV_U' ) {
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cpt
parents:
diff changeset
300 require CPT::Writer::TSV_U;
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cpt
parents:
diff changeset
301 return CPT::Writer::TSV_U->new();
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cpt
parents:
diff changeset
302 }
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cpt
parents:
diff changeset
303 elsif ( $requested eq 'CSV_U' ) {
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cpt
parents:
diff changeset
304 require CPT::Writer::CSV_U;
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cpt
parents:
diff changeset
305 return CPT::Writer::CSV_U->new();
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cpt
parents:
diff changeset
306 }
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cpt
parents:
diff changeset
307 elsif ( $requested eq 'YAML' ) {
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cpt
parents:
diff changeset
308 require CPT::Writer::YAML;
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cpt
parents:
diff changeset
309 return CPT::Writer::YAML->new();
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cpt
parents:
diff changeset
310 }
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cpt
parents:
diff changeset
311 elsif ( $requested eq 'JSON' ) {
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cpt
parents:
diff changeset
312 require CPT::Writer::JSON;
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cpt
parents:
diff changeset
313 return CPT::Writer::JSON->new();
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cpt
parents:
diff changeset
314 }
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cpt
parents:
diff changeset
315 elsif ( $requested eq 'Pandoc' ) {
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cpt
parents:
diff changeset
316 require CPT::Writer::Pandoc;
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cpt
parents:
diff changeset
317 return CPT::Writer::Pandoc->new();
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cpt
parents:
diff changeset
318 }
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cpt
parents:
diff changeset
319 elsif ( $requested eq 'XLS' ) {
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cpt
parents:
diff changeset
320 require CPT::Writer::Spreadsheet::XLS;
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cpt
parents:
diff changeset
321 return CPT::Writer::Spreadsheet::XLS->new();
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cpt
parents:
diff changeset
322 }
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cpt
parents:
diff changeset
323 elsif ( $requested eq 'XLSX' ) {
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cpt
parents:
diff changeset
324 require CPT::Writer::Spreadsheet::XLSX;
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cpt
parents:
diff changeset
325 return CPT::Writer::Spreadsheet::XLSX->new();
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cpt
parents:
diff changeset
326 }
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cpt
parents:
diff changeset
327 elsif ( $requested eq 'TXT' || $requested eq 'CONF' ) {
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cpt
parents:
diff changeset
328 require CPT::Writer::TXT;
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cpt
parents:
diff changeset
329 return CPT::Writer::TXT->new();
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cpt
parents:
diff changeset
330 }
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cpt
parents:
diff changeset
331 elsif ( $acceptable_handlers{$requested} && $format eq 'genomic/annotated'){
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cpt
parents:
diff changeset
332 require CPT::Writer::Genomic;
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cpt
parents:
diff changeset
333 return CPT::Writer::Genomic->new(format => $requested);
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cpt
parents:
diff changeset
334 }
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cpt
parents:
diff changeset
335 elsif ( $requested eq 'Fasta' ) {
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cpt
parents:
diff changeset
336 require CPT::Writer::Fasta;
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cpt
parents:
diff changeset
337 return CPT::Writer::Fasta->new();
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cpt
parents:
diff changeset
338 }
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cpt
parents:
diff changeset
339 elsif ( $requested eq 'GFF3' ) {
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cpt
parents:
diff changeset
340 require CPT::Writer::GFF3;
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cpt
parents:
diff changeset
341 return CPT::Writer::GFF3->new();
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cpt
parents:
diff changeset
342 }
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cpt
parents:
diff changeset
343 elsif ( $requested eq 'HTML' ) {
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cpt
parents:
diff changeset
344 require CPT::Writer::HTML;
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cpt
parents:
diff changeset
345 return CPT::Writer::HTML->new();
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cpt
parents:
diff changeset
346 }
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cpt
parents:
diff changeset
347 elsif ( $requested eq 'SVG' ) {
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cpt
parents:
diff changeset
348 require CPT::Writer::SVG;
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cpt
parents:
diff changeset
349 return CPT::Writer::SVG->new();
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cpt
parents:
diff changeset
350 }
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cpt
parents:
diff changeset
351 elsif ( $requested eq 'PNG' ) {
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cpt
parents:
diff changeset
352 require CPT::Writer::Dummy;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
353 return CPT::Writer::Dummy->new();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
354 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
355 elsif ( $requested eq 'Dummy' ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
356 require CPT::Writer::Dummy;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
357 return CPT::Writer::Dummy->new();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
358 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
359 elsif ( $requested eq 'tar.gz') {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
360 require CPT::Writer::Archive;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
361 return CPT::Writer::Archive->new( format => 'tar.gz' );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
362 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
363 elsif ( $requested eq 'zip') {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
364 require CPT::Writer::Archive;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
365 return CPT::Writer::Archive->new( format => 'zip' );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
366 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
367 elsif ( $requested eq 'tar') {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
368 require CPT::Writer::Archive;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
369 return CPT::Writer::Archive->new( format => 'tar' );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
370 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
371 else {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
372 carp(sprintf("Data Format not yet supported [%s, %s]", $format, $requested));
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
373 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
374 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
375
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
376 # File extension
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
377 has 'extension' => ( is => 'rw', isa => 'Str');
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
378 # What the user said this file was called.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
379 has 'given_filename' => (is => 'rw', isa => 'Str');
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
380
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
381
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
382
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
383
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
384 sub generate_galaxy_variable{
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
385 my ($self) = @_;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
386 unless( -d $self->new_file_path()){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
387 mkdir($self->new_file_path());
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
388 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
389 my $filename =File::Spec->catfile(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
390 $self->new_file_path(),
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
391 sprintf( "primary_%s_%s_visible_%s", $self->files_id(), $self->given_filename(), $self->extension())
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
392 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
393 return $filename;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
394 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
395
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
396
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
397 sub generate_nongalaxy_variable{
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
398 my ($self) = @_;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
399 my $filename =File::Spec->catfile(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
400 sprintf( "%s.%s", $self->given_filename(), $self->extension())
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
401 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
402 return $filename;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
403 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
404
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
405
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
406 sub generate_galaxy_subfile {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
407 my ($self) = @_;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
408 unless( -d $self->files_path()){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
409 mkdir($self->files_path());
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
410 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
411 my $filename =File::Spec->catfile(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
412 $self->files_path,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
413 sprintf( "%s.%s", $self->given_filename(), $self->extension())
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
414 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
415 return $filename;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
416 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
417
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
418
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
419 sub generate_nongalaxy_subfile {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
420 my ($self) = @_;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
421 # they're pretty much equivalent for now
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
422 return $self->generate_galaxy_subfile();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
423 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
424
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
425
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
426 sub get_next_file{
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
427 my ($self) = @_;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
428 my $filename;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
429 if ( $self->galaxy() ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
430 # In which case we want to return the primary output file.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
431 if ( $self->times_called() == 0 ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
432 $filename = $self->parent_filename();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
433 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
434 else {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
435 if ( $self->naming_strategy eq 'sub' ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
436 $filename = $self->generate_galaxy_subfile();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
437 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
438 elsif($self->naming_strategy eq 'var') {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
439 $filename = $self->generate_galaxy_variable();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
440 }else{
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
441 confess("Unknown startegy for multiple output files: " . $self->naming_strategy());
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
442 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
443 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
444 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
445 else # do NOT use galaxy overrides. Paths should be more...sane
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
446 {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
447 # First time we request, should $filename = the primary value, which
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
448 # should be the file they specify.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
449 if ( $self->times_called() == 0 ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
450 $filename = $self->given_filename() . '.' . $self->extension();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
451 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
452 else {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
453 if ( $self->naming_strategy eq 'sub' ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
454 $filename = $self->generate_nongalaxy_subfile();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
455 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
456 elsif($self->naming_strategy eq 'var') {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
457 $filename = $self->generate_nongalaxy_variable();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
458 }else{
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
459 confess("Unknown startegy for multiple output files: " . $self->naming_strategy());
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
460 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
461 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
462 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
463 return $filename;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
464 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
465
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
466 no Moose;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
467 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
468
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
469 __END__
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
470
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
471 =pod
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
472
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
473 =encoding UTF-8
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
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474
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475 =head1 NAME
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parents:
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476
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477 CPT::OutputFiles - Handles script outputs in a sane way, providing facilities to format data and name files for regular use, or in galaxy.
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parents:
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478
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479 =head1 VERSION
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parents:
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480
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481 version 1.99.4
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parents:
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482
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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483 =head1 METHODS
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parents:
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484
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485 =head2 initFromArgs
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parents:
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486
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487 $o->initFromArgs(name => 'GGO_known_output_name', GGO => $GGO);
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parents:
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488
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489 Internal method to intialise data structures from the output id provide in C<name> and the data accessible via the C<GGO> object. You B<must> have already called C<< $GGO->getOptions >>
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parents:
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490
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491 =head2 classyReturnResults
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parents:
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492
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493 # in $GGO->getOptions(
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494 outputs => [
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495 ['html_page', 'HTML output page',
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496 {
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497 validate => 'File/Output',
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498 default => 'aa', # will produce aa.html
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499 data_format => 'text/html',
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500 default_format => 'HTML'
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501 }
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502 ]
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503 ['genbank_download', 'Variable number of GBK files',
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504 {
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505 validate => 'File/Output',
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506 default => 'result', # will produce result.gbk
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507 data_format => 'genomic/annotated',
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508 default_format => 'Genbank'
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509 }
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parents:
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510 ]
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parents:
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511 ]
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512 # )
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513
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514 # Then in your script
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515 $csv_output = CPT::OutputFiles->new(
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516 name => 'html_page',
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517 opt => $options,
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518 );
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519 $csv_output->CRR(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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520 data => $data
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521 );
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522 # Subfile
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523 my $loc = $csv_output->subCRR(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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524 filename => 'cool_picture',
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525 data_format=>'data',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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526 extension=>"png"
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527 );
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528 move($png_file,$loc);
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529
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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530 # You give subfiles a name in case you need to refer to them at any
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531 # point in the parent file.
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532 $csv_output->subCRR(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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533 filename => 'output',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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534 data => $svg_object,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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535 data_format => 'image/svg',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
536 format_as => 'SVG'
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diff changeset
537 );
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parents:
diff changeset
538
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parents:
diff changeset
539
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540 $gbk_output = CPT::OutputFiles->new(
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parents:
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541 name => 'genbank_download',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
542 opt => $options,
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543 );
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parents:
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544 while(my $individual_genbank = $large_seqio->next){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
545 $gbk_output->varCRR(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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546 filename => $individual_genbank->seqid(),
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parents:
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547 data => $individual_genbank,
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parents:
diff changeset
548 );
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parents:
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549 }
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parents:
diff changeset
550
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
551 =head2 _genCRR
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parents:
diff changeset
552
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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553 _genCRR(extension => 'png', data => $data_ref, data_format => 'Dummy',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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554 format_as => 'Dummy', filename => "my-image");
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cpt
parents:
diff changeset
555
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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556 This is an internal method and should not be called directly. It's the end call of all C<CRR>, C<subCRR>, and C<varCRR>. Those methods should be used instead.
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parents:
diff changeset
557
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
558 This method
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parents:
diff changeset
559
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
560 =over 4
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
561
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
562 =item Stores some parameters
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parents:
diff changeset
563
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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564 Specifically C<extension>, C<filename>, C<data_format>, C<format_as>
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parents:
diff changeset
565
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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566 =item Creates a CPT::Writer
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parents:
diff changeset
567
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
568 =item Calls the writer's C<write> method
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parents:
diff changeset
569
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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570 =item returns an array (not arrayref) of filenames
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parents:
diff changeset
571
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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572 These were the filenames that were produced in the writing process. This may be useful for data like CSV data where the output writer may produce N differently named files for each sheet of data.
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parents:
diff changeset
573
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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574 =back
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
575
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
576 =head2 CRR
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parents:
diff changeset
577
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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578 $o->CRR(data => $ref);
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parents:
diff changeset
579
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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580 Writes data to an appropriately named file. (This is usually the "default" parameter supplied in the definition of this output). You should call this method first.
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cpt
parents:
diff changeset
581
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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582 =head2 subCRR
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parents:
diff changeset
583
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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584 $o->subCRR(data => $ref, filename => 'subreport', extension => 'html', data_format => 'text/html', format_as => 'HTML');
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
585
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
586 Writes data to an appropriately named sub file. A subfile is a file that will appear in a folder in the current directory. Subfiles are useful when you want to reference other output files in a primary HTML output or similar. C<subCRR> gives you a method to produce files and have them automatically placed in a sensible location, from which you can reference the files.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
587
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
588 Files are placed in C<< $self->files_path >>. We C<mkdir> this for you, ignoring any errors. If you're paranoid you might want to re-run the mkdir/test for permissions/etc.
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parents:
diff changeset
589
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
590 You must provide
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
591
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
592 =over 4
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
593
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
594 =item filename
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595
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596 name for the output file. You must generate this or it will be named identically to the parent. (And if you call it twice they will clobber each other silently and without mercy)
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597
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598 =item extension
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599
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600 E.g., 'png'
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601
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602 =item data_format
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603
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604 Internal data type. One of the standard C<text/html>, C<genomic/raw>, C<genomic/annotated>, etc.
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605
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606 =item format_as
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607
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608 You're welcome to provide a way to access the format parameter of subfiles to your users, however this is not done for you as there is no way for this module to know ahead of time how many subfiles you will produce.
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609
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610 =back
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611
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612 You may call this method after the first call to CRR or instead of calls to CRR
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613
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614 =head2 varCRR
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615
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616 $o->varCRR(data => $ref, filename => 'subreport', extension => 'html', data_format => 'text/html', format_as => 'HTML');
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617
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618 Writes data to an appropriately named var file. A var file or variable file is much like a subfile, except that in galaxy they will show up as individual history items. Additionally, the default behaviour from the command line is to place all generated files in the current working directory, rather than in a special folder.
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619
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620 You must provide
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621
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622 =over 4
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623
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624 =item filename
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625
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626 name for the output file. You must generate this or it will be named identically to the parent. (And if you call it twice they will clobber each other silently and without mercy)
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627
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628 =item extension
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629
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630 E.g., 'png'
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631
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632 =item data_format
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633
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634 Internal data type. One of the standard C<text/html>, C<genomic/raw>, C<genomic/annotated>, etc.
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635
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636 =item format_as
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637
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638 You're welcome to provide a way to access the format parameter of subfiles to your users, however this is not done for you as there is no way for this module to know ahead of time how many subfiles you will produce.
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639
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640 =back
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641
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642 You may call this method after the first call to CRR or instead of calls to CRR
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643
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644 =head2 bump_times_called
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645
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646 $o->bump_times_called();
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647
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648 Bumps the internal number representing the number of times you've tried to output files for a given output object. This data is used in construction of filenames
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649
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650 =head2 writer_for_format
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651
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652 $o->writer_for_format('text/tabular', 'TSV_U');
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653
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654 Get the appropriate writer class and instantiate it for a given C<data_format> and C<format_as>.
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655
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656 =head2 generate_galaxy_variable
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657
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658 $o->generate_galaxy_variable();
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659
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660 If we need the files to show up as separate History items in galaxy, filenames have to be constructed like this:
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661
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662 =over 4
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663
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664 =item F<$filepath/primary_546_output2_visible_bed>
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665
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666 =item F<$filepath/primary_546_output3_visible_pdf>
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667
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668 =back
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669
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670 where filenames consist of 'primary', an ID number (provided in C<outputname_id> on the command lien), a filename, 'visible', and an extension, all joined with C<_>. Additionally C<$filepath> is generally CWD (I think...)
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671
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672 =head2 generate_nongalaxy_variable
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673
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674 $o->generate_nongalaxy_variable();
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675
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676 =over 4
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677
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678 =item F<$given_filename.$extension>
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679
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680 =back
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681
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682 Parameters are taken from the object variables of the same names.
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683
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684 =head2 generate_galaxy_subfile
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685
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686 $o->generate_galaxy_subfile();
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687
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688 =over 4
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689
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690 =item F<$files_path/$given_filename.$extension>
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691
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692 =back
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693
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694 The paths for images and other files will end up looking something like
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695 F</home/galaxy/galaxy_dist/database/files/000/dataset_56/img1.jpg> with the galaxy provided C<files_path> prepended to the filename.
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696
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697 =head2 generate_nongalaxy_subfile
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698
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699 $o->generate_nongalaxy_subfile();
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700
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701 See L</generate_galaxy_subfile>. Know that the default for C<< $self->files_path >> is C<"outputname.files_path">. It's only "special" when run from inside galaxy.
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702
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703 =head2 get_next_file
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704
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705 $o->get_next_file();
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706
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707 If it's the first time this method has been called, it constructs a default filename. If the C<galaxy> variable is true, then it's just whatever value was passed. Otherwise it's just C<given_filename> and C<extension> put together. C<given_filename> is taken from C<parent_filename>.
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708
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709 If it's not the first time it was called, this module expects you to be using L</varCRR> or L</subCRR> to call (which has set C<naming_strategy>). Those will generate appropriate filenames with calls to one of
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710
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711 =over 4
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712
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713 =item L</generate_galaxy_subfile>
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714
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715 =item L</generate_galaxy_variable>
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716
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717 =item L</generate_nongalaxy_subfile>
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718
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719 =item L</generate_nongalaxy_variable>
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720
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721 =back
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722
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723 based on appropriate variables.
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724
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725 =head1 AUTHOR
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726
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727 Eric Rasche <rasche.eric@yandex.ru>
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728
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729 =head1 COPYRIGHT AND LICENSE
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730
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731 This software is Copyright (c) 2014 by Eric Rasche.
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732
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733 This is free software, licensed under:
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734
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735 The GNU General Public License, Version 3, June 2007
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736
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737 =cut