lib/SGN/Controller/AJAX/Expression.pm

   1
   2 package SGN::Controller::AJAX::Expression;
   3
   4 use Moose;
   5
   6 use strict;
   7 use warnings;
   8
   9 use CXGN::DB::DBICFactory;
  10 use CXGN::GEM::Schema;
  11 use CXGN::GEM::Template;
  12 use CXGN::GEM::Expression;
  13 # use Data::Dumper;
  14
  15 use CXGN::DB::Connection;
  16 use CXGN::GEM::Schema::GeTemplate;
  17 use CXGN::Chado::Dbxref::DbxrefI;
  18
  19 use CXGN::Page::FormattingHelpers qw| page_title_html info_table_html hierarchical_selectboxes_html |;
  20 use CXGN::Page::UserPrefs;
  21
  22 BEGIN { extends 'Catalyst::Controller::REST' }
  23
  24 __PACKAGE__->config(
  25     default => 'application/json',
  26     stash_key => 'rest',
  27     map => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  28    );
  29
  30 our %urlencode;
  31
  32
  33 sub get_data :Path('/tools/expression/result') :Args(0) {
  34     my ($self, $c) = @_;
  35
  36         # declare variables
  37         my @all_data;
  38         my %exp_design;
  39     my $template_id;
  40     my $query_gene = $c->req->param("gene");
  41     $query_gene =~ s/\s+//g;
  42
  43     # to store errors as they happen
  44     my @errors;
  45
  46
  47         # get all data from the query gene
  48     my @schema_list = ('gem', 'biosource', 'metadata', 'public');
  49     my $schema = CXGN::DB::DBICFactory->open_schema( 'CXGN::GEM::Schema', search_path => \@schema_list, );
  50     my @template_array = CXGN::GEM::Template->new_by_name($schema, $query_gene);
  51
  52
  53
  54     ## Add expression object
  55     foreach my $template (@template_array) {
  56                 if (!defined $template || !defined $template->get_template_id()) {
  57                         push (@errors, "The query gene is not available in our database. Please try again\n");
  58                 } else {
  59                         $template_id = $template->get_template_id();
  60                         print "id: $template_id\n";
  61
  62                         # get the experiment data from each experiment
  63                         my ($exp_data, $design_name, $design_desc, $exp_dbxref,$exp_pub) = get_expression_data($template_id,$schema);
  64
  65                         $exp_design{"name"} = $design_name;
  66                         $exp_design{"description"} = $design_desc;
  67                         $exp_design{"dbxref"} = $exp_dbxref;
  68                         $exp_design{"pub"} = $exp_pub;
  69                         $exp_design{"data"} = $exp_data;
  70
  71                         # save the final structure of data; An array containing one hash for each experiment
  72                         push(@all_data, \%exp_design);
  73                 }
  74     }
  75
  76         # print STDERR "my data: ".Dumper(@all_data)."\n";
  77         # print STDERR "my data: ".Dumper($all_data[0]{"data"})."\n";
  78
  79
  80 #   print STDERR "final design:".Dumper(@all_design_data)."\n";
  81
  82         # return errors if needed
  83     if (scalar (@errors) > 0){
  84                 my $user_errors = join("<br />", @errors);
  85                 $c->stash->{rest} = {error => $user_errors};
  86                 return;
  87     }
  88
  89         # return dat to mason view
  90     $c->stash->{rest} = {
  91                 gene_id => $template_id,
  92                 gene_name => $query_gene,
  93                 all_exp_design =>\@all_data,
  94     };
  95
  96 }
  97
  98
  99
 100 sub get_expression_data {
 101     my $template_id = shift;
 102     my $schema = shift;
 103     my @one_design;
 104     my @one_experiment;
 105     my $experiment;
 106
 107         my $title;
 108         my $journal;
 109         my $pyear;
 110
 111         #----------------------------------
 112         my %one_exp;
 113         my @all_exp;
 114         my @all_data;
 115         #----------------------------------
 116
 117     my @exp_exp_values_rows = $schema->resultset('GeExpressionByExperiment')
 118                                      ->search( { template_id => $template_id } );
 119
 120 #   print STDERR "rows: ".Dumper(@exp_exp_values_rows)."\n";
 121
 122         foreach my $expexp_value_row (@exp_exp_values_rows) {
 123                 my %exp_values = $expexp_value_row->get_columns();
 124
 125                 my $exp_id = $exp_values{'experiment_id'};
 126                 $one_experiment[0] = $exp_id;
 127
 128                 $experiment = CXGN::GEM::Experiment->new($schema, $exp_id);
 129
 130                 if (defined $experiment && defined $experiment->get_experiment_id() ) {
 131
 132                         my $exp_name = $experiment->get_experiment_name();
 133 #                       print STDERR "\nEXP_NAME: $exp_name\n";
 134
 135                         my $exp_rep = $exp_values{'replicates_used'} || 'NA';
 136
 137                         my $fpkm = Math::BigFloat->new( $exp_values{'mean'})
 138                                          ->ffround(-2)
 139                                          ->bstr();
 140
 141                         # my $median = Math::BigFloat->new( $exp_values{'median'} )
 142                         #                                            ->ffround(-2)
 143                         #                  ->bstr();
 144
 145                         my $fpkm_lo = Math::BigFloat->new($exp_values{'standard_desviation'})
 146                                        ->ffround(-2)
 147                                        ->bstr();
 148
 149                         my $fpkm_hi = Math::BigFloat->new($exp_values{'coefficient_of_variance'})
 150                                        ->ffround(-2)
 151                                        ->bstr();
 152
 153                         $one_exp{"name"} = $exp_name;
 154                         $one_exp{"id"} = $exp_id;
 155                         $one_exp{"replicates"} = $exp_rep;
 156                         $one_exp{"fpkm"} = $fpkm;
 157                         $one_exp{"fpkm_lo"} = $fpkm_lo;
 158                         $one_exp{"fpkm_hi"} = $fpkm_hi;
 159                         $one_exp{"exp_description"} = $experiment->get_description();
 160
 161
 162
 163                     ## Get the external links for experiment conditions
 164                      my @exp_dbxref_ids = $experiment->get_dbxref_list();
 165                          my $exp_dbxref_html = "";
 166
 167                      foreach my $dbxref_id (@exp_dbxref_ids) {
 168                                  $exp_dbxref_html = "$exp_dbxref_html ".get_dbxref_html($dbxref_id, $schema);
 169                      }
 170
 171                          print STDERR "SRA dbxref: $exp_dbxref_html\n";
 172                         $one_exp{"exp_links"} = $exp_dbxref_html;
 173
 174
 175 #           my @target_list = $experiment->get_target_list();
 176 #           my $tissue = set_tissue($target_list[0]);
 177
 178                 }
 179         #       print STDERR "one exp:".Dumper(@one_experiment)."\n";
 180                 my %tmp_hash = %one_exp;
 181                 push (@all_exp, \%tmp_hash);
 182                 # %one_exp;
 183
 184
 185                 # push (@all_exp, %one_exp);
 186                 # %one_exp;
 187     }
 188
 189     my $expdesign = $experiment->get_experimental_design();
 190     my $expdesign_name = $expdesign->get_experimental_design_name();
 191     my $expdesign_desc = $expdesign->get_description();
 192         my $pub_html = '';
 193         my $expdesign_dbxref_html = '';
 194
 195     #print STDERR "$expdesign_name: experiment replicates: $exp_rep\n\n";
 196
 197         # get exp_design publications
 198         my @pub_id_list = $expdesign->get_publication_list();
 199         # my @pub_title_list = $expdesign->get_publication_list('title');
 200         # my @pub_journal_list = $expdesign->get_publication_list('series_name');
 201         # my @pub_year_list = $expdesign->get_publication_list('pyear');
 202
 203
 204
 205         my @dbxref_id_list = $expdesign->get_dbxref_list();
 206
 207         for (my $i = 0; $i < scalar(@pub_id_list); $i++) {
 208                 if ($pub_id_list[$i]) {
 209
 210                         $expdesign_dbxref_html = "$expdesign_dbxref_html ".get_dbxref_html($dbxref_id_list[$i], $schema);
 211
 212
 213                         my ($pub_obj) = $schema->resultset('Pub::Pub')
 214                                                        ->search({ pub_id => $pub_id_list[$i]});
 215
 216
 217                         $title = $pub_obj->get_column('title');
 218                         $journal = $pub_obj->get_column('series_name');
 219                         $pyear = $pub_obj->get_column('pyear');
 220
 221
 222                 }
 223                 if ($title && $journal && $pyear) {
 224                         $pub_html = "$pub_html $title $journal $pyear.<br/>\n";
 225                 }
 226                 elsif ($title) {
 227                         $pub_html = "$pub_html $title<br/>\n";
 228                 }
 229
 230         }
 231         # print STDERR "$expdesign_dbxref_html\n";
 232
 233         # my $exp_design_description = "<b>$expdesign_name:</b> $expdesign_desc.";
 234
 235         # if ($expdesign_dbxref_html ne '') {
 236         #       $exp_design_description = "$exp_design_description\n<br/><b>External links:</b> $expdesign_dbxref_html\n";
 237         #       # $exp_design_description = "$exp_design_description\n<b>External link:</b> $pub_dbxref_html\n";
 238         # }
 239         # if ($pub_dbxref_html ne '') {
 240         #       $exp_design_description = "$exp_design_description\n<br/><b>Publications:</b> $pub_dbxref_html\n";
 241         #       # $exp_design_description = "$exp_design_description\n<b>External link:</b> $pub_dbxref_html\n";
 242         # }
 243
 244         # push (@all_data, %exp_design);
 245
 246     return (\@all_exp,$expdesign_name,$expdesign_desc,$expdesign_dbxref_html,$pub_html);
 247     # return (\@one_design,$expdesign_name);
 248 }
 249
 250 sub get_dbxref_html {
 251         my $dbxref_id = shift;
 252         my $schema = shift;
 253         my $dbxref_html;
 254
 255         my ($dbxref_obj) = $schema->resultset('General::Dbxref')
 256                                       ->search({ dbxref_id => $dbxref_id });
 257
 258         if (defined $dbxref_obj) {
 259             my ($db_obj) = $schema->resultset('General::Db')
 260                                       ->search({ db_id => $dbxref_obj->get_column('db_id') });
 261
 262             my $dbxref_url = $db_obj->get_column('urlprefix').$db_obj->get_column('url').$dbxref_obj->get_column('accession');
 263             $dbxref_html = "<a href='".$dbxref_url."'  target='_blank'>".$db_obj->get_column('name').":".$dbxref_obj->get_column('accession')."</a>";
 264         }
 265
 266         return $dbxref_html;
 267 }
 268
 269
 270 sub set_tissue {
 271     my $first_target = shift;
 272     my $dbh = CXGN::DB::Connection->new();
 273     my $tissue;
 274     my @sample_list = $first_target->get_sample_list();
 275
 276     foreach my $sample (@sample_list) {
 277         my %po = $sample_list[0]->get_dbxref_related('PO');
 278
 279         foreach my $sample_dbxref_id (keys %po) {
 280             my %dbxref_po = %{ $po{$sample_dbxref_id} };
 281             my $po_name = $dbxref_po{'cvterm.name'};
 282
 283             my $cvterm = CXGN::Chado::Cvterm->new( $dbh, $dbxref_po{'cvterm.cvterm_id'} );
 284             my $accession   = $cvterm->get_accession;
 285
 286 #           print STDERR "$accession: $po_name\n";
 287         }
 288     }
 289     return $tissue;
 290 }
 291
 292
 293
 294 1;