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' },
  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 $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  61     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado', $sp_person_id);
  62     my @trial_ids = @{_parse_list_from_json($c->req->param('trial_ids'))};
  63     #print STDERR Dumper \@trial_ids;
  64     my $format = $c->req->param('format') || "ExcelBasic";
  65     my $include_notes = $c->req->param('include_notes');
  66     my $data_level = $c->req->param('data_level') || "plots";
  67     my $file_format = $c->req->param('create_spreadsheet_phenotype_file_format') || "detailed";
  68     my $sample_number = $c->req->param('sample_number');
  69     if ($sample_number eq '') {$sample_number = undef};
  70     my $predefined_columns = $c->req->param('predefined_columns') ? decode_json $c->req->param('predefined_columns') : [];
  71     my $trial_stock_type = $c->req->param('trial_stock_type');
  72     #print STDERR Dumper $sample_number;
  73     #print STDERR Dumper $predefined_columns;
  74
  75     my $trial_name = "";
  76     foreach (@trial_ids){
  77         my $trial = CXGN::Trial->new( { bcs_schema => $c->dbic_schema("Bio::Chado::Schema", undef, $sp_person_id), trial_id => $_ });
  78               $trial_name = $trial->get_name();
  79               $trial_name =~ s/ /\_/g;
  80
  81         if ($data_level eq 'plants') {
  82             if (!$trial->has_plant_entries()) {
  83                 $c->stash->{rest} = { error => "The requested trial (".$trial->get_name().") does not have plant entries. Please create the plant entries first." };
  84                 return;
  85             }
  86         }
  87         if ($data_level eq 'subplots' || $data_level eq 'plants_subplots') {
  88             if (!$trial->has_subplot_entries()) {
  89                 $c->stash->{rest} = { error => "The requested trial (".$trial->get_name().") does not have subplot entries." };
  90                 return;
  91             }
  92         }
  93         if ($data_level eq 'tissue_samples') {
  94             if (!$trial->has_tissue_sample_entries()) {
  95                 $c->stash->{rest} = { error => "The requested trial (".$trial->get_name().") does not have tissue sample entries. Please create the tissue sample entries first." };
  96                 return;
  97             }
  98         }
  99     }
 100
 101     my @trait_list = @{_parse_list_from_json($c->req->param('trait_list'))};
 102     my $dir = $c->tempfiles_subdir('/download');
 103     my $rel_file = $c->tempfile( TEMPLATE => "download/$trial_name"."_phenotype_collectionXXXX");
 104     $rel_file = substr $rel_file, 0, -4;
 105     my $tempfile = $c->config->{basepath}."/".$rel_file.".xlsx";
 106     my $create_spreadsheet = CXGN::Trial::Download->new({
 107         bcs_schema => $schema,
 108         trial_list => \@trial_ids,
 109         trait_list => \@trait_list,
 110         filename => $tempfile,
 111         format => $format,
 112         data_level => $data_level,
 113         include_notes => $include_notes,
 114         sample_number => $sample_number,
 115         predefined_columns => $predefined_columns,
 116         trial_stock_type => $trial_stock_type,
 117     });
 118
 119     $create_spreadsheet->download();
 120
 121     print STDERR "DOWNLOAD FILENAME = ".$create_spreadsheet->filename()."\n";
 122     print STDERR "RELATIVE  = $rel_file\n";
 123
 124     #Add postcomposed terms from selected predefined_columns
 125     if (scalar(@$predefined_columns)>0){
 126         my @allowed_composed_cvs = split ',', $c->config->{composable_cvs};
 127         my $composable_cvterm_delimiter = $c->config->{composable_cvterm_delimiter};
 128         my $composable_cvterm_format = $c->config->{composable_cvterm_format};
 129         my @allowed_composed_cvs_minus_trait = grep { $_ ne 'trait' } @allowed_composed_cvs;
 130         my %id_hash;
 131         for my $i (0 .. scalar @$predefined_columns){
 132             my $cv_type = $allowed_composed_cvs_minus_trait[$i];
 133             foreach my $selected_term (values %{$predefined_columns->[$i]}){
 134                 my $cvterm_id = SGN::Model::Cvterm->get_cvterm_row_from_trait_name($schema, $selected_term)->cvterm_id();
 135                 push @{$id_hash{$cv_type}}, $cvterm_id;
 136             }
 137         }
 138         my @trait_cvterm_ids;
 139         foreach (@trait_list){
 140             push @trait_cvterm_ids, SGN::Model::Cvterm->get_cvterm_row_from_trait_name($schema, $_)->cvterm_id();
 141         }
 142         $id_hash{'trait'} = \@trait_cvterm_ids;
 143         #print STDERR Dumper \%id_hash;
 144         my $traits = SGN::Model::Cvterm->get_traits_from_component_categories($schema, \@allowed_composed_cvs, $composable_cvterm_delimiter, $composable_cvterm_format, \%id_hash);
 145         my %new_traits;
 146         foreach (@{$traits->{new_traits}}){
 147             $new_traits{$_->[1]} = join ',', @{$_->[0]};
 148         }
 149         #print STDERR Dumper \%new_traits;
 150         my $new_terms;
 151         eval {
 152             my $onto = CXGN::Onto->new({ schema => $schema });
 153             $new_terms = $onto->store_composed_term(\%new_traits);
 154         };
 155         if ($@) {
 156             die "An error occurred saving the new trait details: $@";
 157         }
 158         #print STDERR Dumper $new_terms;
 159     }
 160
 161     $c->stash->{rest} = { filename => $urlencode{$rel_file.".xlsx"} };
 162 }
 163
 164 sub _parse_list_from_json {
 165   my $list_json = shift;
 166   my $json = new JSON;
 167   if ($list_json) {
 168       #my $decoded_list = $json->allow_nonref->utf8->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($list_json);
 169       my $decoded_list = decode_json($list_json);
 170     my @array_of_list_items = @{$decoded_list};
 171     return \@array_of_list_items;
 172   }
 173   else {
 174     return;
 175   }
 176 }
 177
 178 #########
 179 1;
 180 #########