lib/SGN/Controller/AJAX/TrialComparison.pm

   1
   2 use strict;
   3
   4 package SGN::Controller::AJAX::TrialComparison;
   5
   6 use Moose;
   7 use Data::Dumper;
   8 use File::Temp qw | tempfile |;
   9 use File::Slurp;
  10 use CXGN::Dataset;
  11 use SGN::Model::Cvterm;
  12 use CXGN::List;
  13 use CXGN::List::Validate;
  14 use CXGN::Trial::Download;
  15 use CXGN::Phenotypes::PhenotypeMatrix;
  16 use CXGN::BreederSearch;
  17 use Cwd qw(cwd);
  18
  19 BEGIN { extends 'Catalyst::Controller::REST' }
  20
  21 __PACKAGE__->config(
  22     default   => 'application/json',
  23     stash_key => 'rest',
  24     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  25    );
  26
  27
  28 has 'schema' => (
  29                  is       => 'rw',
  30                  isa      => 'DBIx::Class::Schema',
  31                  lazy_build => 1,
  32                 );
  33
  34
  35 # /ajax/trial/compare?trial_id=345&trial_id=4848&trial_id=38484&cvterm_id=84848
  36
  37 sub compare_trail_list_data_test : Path('/ajax/trial/compare_list_data_test') : ActionClass('REST') {}
  38
  39 sub compare_trail_list_data_test_GET : Args(0) {
  40     my $self = shift;
  41     my $c = shift;
  42     my $result = `python bin/test/TrialComparisonFakeDataGen.py`;#`python TrialComparison_test.py`;
  43     my $cvterm_id = "TEST_TEST";
  44     $c->stash->{rest} = { csv => $result, cvterm_id => $cvterm_id};
  45 }
  46
  47 sub compare_trail_list_data : Path('/ajax/trial/compare_list_data') : ActionClass('REST') {}
  48
  49 sub compare_trail_list_data_GET : Args(0) {
  50     my $self = shift;
  51     my $c = shift;
  52
  53     my $list_id = $c->req->param("list_id");
  54
  55     my $user = $c->user();
  56
  57     if (!$user) {
  58         $c->stash->{rest} = { error => "Must be logged in to use functionality associated with lists." };
  59         return;
  60     }
  61
  62     my $user_id = $user->get_object()->get_sp_person_id();
  63
  64     print STDERR "USER ID : $user_id\n";
  65
  66     if (!$list_id) {
  67         $c->stash->{rest} = { error => "Error: No list_id provided." };
  68         return;
  69     }
  70
  71     my $cvterm_id = $c->req->param("cvterm_id");
  72
  73     if (!$cvterm_id) {
  74         $c->stash->{rest} = { error => "Error: No cvterm_id provided." };
  75         return;
  76     }
  77
  78     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  79
  80     my $v = CXGN::List::Validate->new();
  81     my $r = $v->validate($schema, "trial", $list_id);
  82
  83     if ($r->{missing}) {
  84         $c->stash->{rest} = { error => "Not all trials could be found in the database." };
  85         return;
  86     }
  87
  88     my $dbh = $schema->storage()->dbh();
  89     my $tl = CXGN::List->new({ dbh => $dbh, list_id => $list_id, owner => $user_id });
  90
  91     if (! $tl) {
  92         $c->stash->{rest} = { error => "The specified list does not exist, is not owned by you, or is not a trial list" };
  93         return;
  94     }
  95
  96     my $trials = $tl->elements();
  97
  98     my $trial_id_rs = $schema->resultset("Project::Project")->search( { name => { in => [ @$trials ]} });
  99
 100     my @trial_ids = map { $_->project_id() } $trial_id_rs->all();
 101
 102     if (@trial_ids < 2) {
 103         $c->stash->{rest} = { error => "One or both trials are not found in the database. Please try again." };
 104         return;
 105     }
 106
 107     my $csv_loc = $self->make_csv($c, $cvterm_id, @trial_ids);
 108     my $csv = read_file($c->config->{basepath}."/".$csv_loc);
 109     $c->stash->{rest} = { csv => $csv, cvterm_id => $cvterm_id };
 110 }
 111
 112 sub make_csv {
 113     my $self = shift;
 114     my $c = shift;
 115     my $cvterm_id = shift;
 116     my @trial_ids = @_;
 117
 118     my $schema = $c->dbic_schema("Bio::Chado::Schema");
 119
 120     $c->tempfiles_subdir("compare_trials");
 121
 122      my ($fh, $tempfile) = $c->tempfile(TEMPLATE=>"compare_trials/trial_phenotypes_download_XXXXX");
 123
 124     my $temppath = $c->config->{basepath}."/".$tempfile;
 125
 126     my $download = CXGN::Trial::Download->new({
 127         bcs_schema => $c->dbic_schema("Bio::Chado::Schema"),
 128         trial_list => \@trial_ids,
 129         trait_list => [ $cvterm_id ],
 130         filename => $temppath,
 131         format => 'TrialPhenotypeCSV',
 132         data_level => 'plot', #'plot' or 'plant' or 'all'. CXGN::Dataset would default to 'plot'
 133         search_type=> 'complete', #'complete' or 'fast'. CXGN::Dataset would default to 'fast'
 134         has_header => 0
 135     });
 136     my $error = $download->download();
 137     my $errorfile = $temppath.".err";
 138     if (-e $errorfile) {
 139         my $error = read_file($errorfile);
 140         $c->stash->{rest} = { error => $error };
 141         return;
 142     }
 143     my $file = $tempfile.""; # convert from object to string
 144     return ($tempfile);
 145 }
 146
 147 sub common_traits : Path('/ajax/trial/common_traits') : ActionClass('REST') {}
 148
 149 sub common_traits_GET : Args(0) {
 150     my $self = shift;
 151     my $c = shift;
 152
 153     my @trials = $c->req->param("trial_id");
 154
 155     $self->get_common_traits($c, @trials);
 156 }
 157
 158
 159 sub get_common_traits {
 160     my $self = shift;
 161     my $c = shift;
 162     my @trials = @_;
 163     my $schema = $c->dbic_schema("Bio::Chado::Schema");
 164     print STDERR '@trials: '.Dumper(@trials);
 165     my $trials_string = "\'".join( "\',\'",@trials)."\'";
 166     print STDERR '$trials_string: '.Dumper($trials_string);
 167     my @criteria = ['trials','traits'];
 168     my %dataref;
 169     my %queryref;
 170     $dataref{traits}->{trials} = $trials_string;
 171     $queryref{traits}->{trials} = 1;
 172     print STDERR 'data: '.Dumper(\%dataref);
 173     print STDERR 'query: '.Dumper(\%queryref);
 174     my $breedersearch =  CXGN::BreederSearch->new({"dbh"=>$c->dbc->dbh});
 175     my $results_ref = $breedersearch->metadata_query(@criteria, \%dataref, \%queryref);
 176     print STDERR "Results: \n";
 177     #print STDERR Dumper($results_ref);
 178     $c->stash->{rest} = {
 179         options => $results_ref->{results},
 180       list_trial_count=> scalar(@trials),
 181       common_trait_count => scalar(@{$results_ref->{results}}),
 182     };
 183 }
 184
 185 1;