lib/SGN/Controller/AJAX/TissueSample.pm

   1
   2 =head1 NAME
   3
   4 SGN::Controller::AJAX::TissueSample - a REST controller class to provide tissue sample functionality
   5
   6 =head1 DESCRIPTION
   7
   8
   9 =head1 AUTHOR
  10
  11 =cut
  12
  13 package SGN::Controller::AJAX::TissueSample;
  14
  15 use Moose;
  16 use Data::Dumper;
  17 use JSON;
  18 use CXGN::People::Login;
  19 use CXGN::Trial::Search;
  20 use JSON;
  21
  22 BEGIN { extends 'Catalyst::Controller::REST' }
  23
  24 __PACKAGE__->config(
  25     default   => 'application/json',
  26     stash_key => 'rest',
  27     map       => { 'application/json' => 'JSON' },
  28    );
  29
  30 sub tissue_sample_field_trials : Path('/ajax/tissue_samples/field_trials') : ActionClass('REST') { }
  31
  32 sub tissue_sample_field_trials_GET : Args(0) {
  33     my $self = shift;
  34     my $c = shift;
  35     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  36
  37     my $trial_search = CXGN::Trial::Search->new({
  38         bcs_schema=>$bcs_schema,
  39         trial_has_tissue_samples=>1,
  40     });
  41     my ($data, $total_count) = $trial_search->search();
  42     my @result;
  43     my %selected_columns = ('tissue_sample_name'=>1, 'tissue_sample_id'=>1, 'plant_name'=>1, 'plot_name'=>1, 'block_number'=>1, 'plant_number'=>1, 'plot_number'=>1, 'rep_number'=>1, 'row_number'=>1, 'col_number'=>1, 'accession_name'=>1, 'is_a_control'=>1);
  44     my $selected_columns_json = encode_json \%selected_columns;
  45     foreach (@$data){
  46         my $folder_string = '';
  47         if ($_->{folder_name}){
  48             $folder_string = "<a href=\"/folder/$_->{folder_id}\">$_->{folder_name}</a>";
  49         }
  50         push @result,
  51           [
  52             "<a href=\"/breeders_toolbox/trial/$_->{trial_id}\">$_->{trial_name}</a>",
  53             $_->{description},
  54             "<a href=\"/breeders/program/$_->{breeding_program_id}\">$_->{breeding_program_name}</a>",
  55             $folder_string,
  56             $_->{year},
  57             $_->{location_name},
  58             $_->{trial_type},
  59             $_->{design},
  60             $_->{project_planting_date},
  61             $_->{project_harvest_date},
  62             "<a class='btn btn-sm btn-default' href='/breeders/trial/$_->{trial_id}/download/layout?format=csv&dataLevel=field_trial_tissue_samples&selected_columns=$selected_columns_json'>Download Layout</a>"
  63           ];
  64     }
  65     #print STDERR Dumper \@result;
  66
  67     $c->stash->{rest} = { data => \@result };
  68 }
  69
  70 sub tissue_sample_genotyping_trials : Path('/ajax/tissue_samples/genotyping_trials') : ActionClass('REST') { }
  71
  72 sub tissue_sample_genotyping_trials_GET : Args(0) {
  73     my $self = shift;
  74     my $c = shift;
  75     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  76
  77     my $trial_search = CXGN::Trial::Search->new({
  78         bcs_schema=>$bcs_schema,
  79         trial_design_list=>['genotyping_plate']
  80     });
  81     my ($data, $total_count) = $trial_search->search();
  82     my @result;
  83     foreach (@$data){
  84         my $folder_string = '';
  85         if ($_->{folder_name}){
  86             $folder_string = "<a href=\"/folder/$_->{folder_id}\">$_->{folder_name}</a>";
  87         }
  88         push @result,
  89           [
  90             "<a href=\"/breeders_toolbox/trial/$_->{trial_id}\">$_->{trial_name}</a>",
  91             $_->{description},
  92             "<a href=\"/breeders/program/$_->{breeding_program_id}\">$_->{breeding_program_name}</a>",
  93             $folder_string,
  94             $_->{year},
  95             $_->{location_name},
  96             $_->{genotyping_facility},
  97             $_->{genotyping_plate_format},
  98             $_->{genotyping_plate_sample_type},
  99             "<a class='btn btn-sm btn-default' href='/breeders/trial/$_->{trial_id}/download/layout?format=csv&dataLevel=plate'>Download Layout</a>"
 100           ];
 101     }
 102     #print STDERR Dumper \@result;
 103
 104     $c->stash->{rest} = { data => \@result };
 105 }
 106
 107 sub tissue_sample_sampling_trials : Path('/ajax/tissue_samples/sampling_trials') : ActionClass('REST') { }
 108
 109 sub tissue_sample_sampling_trials_GET : Args(0) {
 110     my $self = shift;
 111     my $c = shift;
 112     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 113
 114     my $trial_search = CXGN::Trial::Search->new({
 115         bcs_schema=>$bcs_schema,
 116         trial_design_list=>['sampling_trial']
 117     });
 118     my ($data, $total_count) = $trial_search->search();
 119     my @result;
 120     foreach (@$data){
 121         my $folder_string = '';
 122         if ($_->{folder_name}){
 123             $folder_string = "<a href=\"/folder/$_->{folder_id}\">$_->{folder_name}</a>";
 124         }
 125         push @result,
 126           [
 127             "<a href=\"/breeders_toolbox/trial/$_->{trial_id}\">$_->{trial_name}</a>",
 128             $_->{description},
 129             "<a href=\"/breeders/program/$_->{breeding_program_id}\">$_->{breeding_program_name}</a>",
 130             $folder_string,
 131             $_->{year},
 132             $_->{location_name},
 133             $_->{sampling_facility},
 134             $_->{sampling_trial_sample_type},
 135             "<a class='btn btn-sm btn-default' href='/breeders/trial/$_->{trial_id}/download/layout?format=csv&dataLevel=samplingtrial'>Download Layout</a>"
 136           ];
 137     }
 138     #print STDERR Dumper \@result;
 139
 140     $c->stash->{rest} = { data => \@result };
 141 }
 142
 143 1;