lib/SGN/Controller/AJAX/PhenotypesDownload.pm

   1
   2 =head1 NAME
   3
   4 SGN::Controller::AJAX::PhenotypesDownload - a REST controller class to provide the
   5 backend for downloading phenotype spreadsheets
   6
   7 =head1 DESCRIPTION
   8
   9 Downloading Phenotype Spreadsheets
  10
  11 =head1 AUTHOR
  12
  13 Jeremy Edwards <jde22@cornell.edu>
  14
  15 =cut
  16
  17 package SGN::Controller::AJAX::PhenotypesDownload;
  18
  19 use Moose;
  20 use Try::Tiny;
  21 use DateTime;
  22 use File::Slurp;
  23 use File::Spec::Functions;
  24 use File::Copy;
  25 use List::MoreUtils qw /any /;
  26 use SGN::View::ArrayElements qw/array_elements_simple_view/;
  27 use CXGN::Stock::StockTemplate;
  28 use JSON -support_by_pp;
  29 use CXGN::Phenotypes::CreateSpreadsheet;
  30 use CXGN::Trial::Download;
  31 use Tie::UrlEncoder; our(%urlencode);
  32 use Data::Dumper;
  33 use JSON qw( decode_json );
  34
  35 BEGIN { extends 'Catalyst::Controller::REST' }
  36
  37 __PACKAGE__->config(
  38     default   => 'application/json',
  39     stash_key => 'rest',
  40     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  41    );
  42
  43
  44 sub create_phenotype_spreadsheet :  Path('/ajax/phenotype/create_spreadsheet') : ActionClass('REST') { }
  45
  46 sub create_phenotype_spreadsheet_GET : Args(0) {
  47     my $self = shift;
  48     my $c = shift;
  49     $c->forward('create_phenotype_spreadsheet_POST');
  50 }
  51
  52 sub create_phenotype_spreadsheet_POST : Args(0) {
  53   print STDERR "phenotype download controller\n";
  54   my ($self, $c) = @_;
  55   if (!$c->user()) {
  56     $c->stash->{rest} = {error => "You need to be logged in to download a phenotype spreadsheet." };
  57     return;
  58   }
  59
  60   my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  61   my @trial_ids = @{_parse_list_from_json($c->req->param('trial_ids'))};
  62   print STDERR Dumper \@trial_ids;
  63   my $format = $c->req->param('format') || "ExcelBasic";
  64   my $data_level = $c->req->param('data_level') || "plots";
  65   my $file_format = $c->req->param('create_spreadsheet_phenotype_file_format') || "detailed";
  66   my $sample_number = $c->req->param('sample_number');
  67   if ($sample_number eq '') {$sample_number = undef};
  68   my $predefined_columns = $c->req->param('predefined_columns') ? decode_json $c->req->param('predefined_columns') : [];
  69
  70   #print STDERR Dumper $sample_number;
  71   #print STDERR Dumper $predefined_columns;
  72
  73   foreach (@trial_ids){
  74       if ($data_level eq 'plants') {
  75           my $trial = CXGN::Trial->new( { bcs_schema => $c->dbic_schema("Bio::Chado::Schema"), trial_id => $_ });
  76           if (!$trial->has_plant_entries()) {
  77               $c->stash->{rest} = { error => "The requested trial (".$trial->get_name().") does not have plant entries. Please create the plant entries first." };
  78               return;
  79           }
  80       }
  81       if ($data_level eq 'subplots' || $data_level eq 'plants_subplots') {
  82           my $trial = CXGN::Trial->new( { bcs_schema => $c->dbic_schema("Bio::Chado::Schema"), trial_id => $_ });
  83           if (!$trial->has_subplot_entries()) {
  84               $c->stash->{rest} = { error => "The requested trial (".$trial->get_name().") does not have subplot entries." };
  85               return;
  86           }
  87       }
  88   }
  89
  90   my @trait_list = @{_parse_list_from_json($c->req->param('trait_list'))};
  91   my $dir = $c->tempfiles_subdir('/download');
  92   my $rel_file = $c->tempfile( TEMPLATE => 'download/downloadXXXXX');
  93   my $tempfile = $c->config->{basepath}."/".$rel_file.".xls";
  94
  95   my $create_spreadsheet = CXGN::Trial::Download->new(
  96       {
  97           bcs_schema => $schema,
  98           trial_list => \@trial_ids,
  99           trait_list => \@trait_list,
 100           filename => $tempfile,
 101           format => $format,
 102       data_level => $data_level,
 103       sample_number => $sample_number,
 104       predefined_columns => $predefined_columns,
 105       });
 106
 107      $create_spreadsheet->download();
 108
 109     print STDERR "DOWNLOAD FILENAME = ".$create_spreadsheet->filename()."\n";
 110     print STDERR "RELATIVE  = $rel_file\n";
 111
 112     #Add postcomposed terms from selected predefined_columns
 113     if (scalar(@$predefined_columns)>0){
 114         my @allowed_composed_cvs = split ',', $c->config->{composable_cvs};
 115         my $composable_cvterm_delimiter = $c->config->{composable_cvterm_delimiter};
 116         my $composable_cvterm_format = $c->config->{composable_cvterm_format};
 117         my @allowed_composed_cvs_minus_trait = grep { $_ ne 'trait' } @allowed_composed_cvs;
 118         my %id_hash;
 119         for my $i (0 .. scalar @$predefined_columns){
 120             my $cv_type = $allowed_composed_cvs_minus_trait[$i];
 121             foreach my $selected_term (values %{$predefined_columns->[$i]}){
 122                 my $cvterm_id = SGN::Model::Cvterm->get_cvterm_row_from_trait_name($schema, $selected_term)->cvterm_id();
 123                 push @{$id_hash{$cv_type}}, $cvterm_id;
 124             }
 125         }
 126         my @trait_cvterm_ids;
 127         foreach (@trait_list){
 128             push @trait_cvterm_ids, SGN::Model::Cvterm->get_cvterm_row_from_trait_name($schema, $_)->cvterm_id();
 129         }
 130         $id_hash{'trait'} = \@trait_cvterm_ids;
 131         #print STDERR Dumper \%id_hash;
 132         my $traits = SGN::Model::Cvterm->get_traits_from_component_categories($schema, \@allowed_composed_cvs, $composable_cvterm_delimiter, $composable_cvterm_format, \%id_hash);
 133         my %new_traits;
 134         foreach (@{$traits->{new_traits}}){
 135             $new_traits{$_->[1]} = join ',', @{$_->[0]};
 136         }
 137         #print STDERR Dumper \%new_traits;
 138         my $new_terms;
 139         eval {
 140             my $onto = CXGN::Onto->new({ schema => $schema });
 141             $new_terms = $onto->store_composed_term(\%new_traits);
 142         };
 143         if ($@) {
 144             die "An error occurred saving the new trait details: $@";
 145         }
 146         #print STDERR Dumper $new_terms;
 147     }
 148
 149 #if ($error) {
 150 #$c->stash->{rest} = { error => $error };
 151 #return;
 152 #}
 153     $c->stash->{rest} = { filename => $urlencode{$rel_file.".xls"} };
 154
 155 }
 156
 157 sub _parse_list_from_json {
 158   my $list_json = shift;
 159   my $json = new JSON;
 160   if ($list_json) {
 161     my $decoded_list = $json->allow_nonref->utf8->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($list_json);
 162     #my $decoded_list = decode_json($list_json);
 163     my @array_of_list_items = @{$decoded_list};
 164     return \@array_of_list_items;
 165   }
 166   else {
 167     return;
 168   }
 169 }
 170
 171 #########
 172 1;
 173 #########