lib/SGN/Controller/AJAX/BreederSearch.pm

   1
   2 package SGN::Controller::AJAX::BreederSearch;
   3
   4 use Moose;
   5
   6 use List::MoreUtils qw | any all |;
   7 use JSON::Any;
   8 use Data::Dumper;
   9 use Try::Tiny;
  10 use CXGN::BreederSearch;
  11
  12 BEGIN { extends 'Catalyst::Controller::REST'; };
  13
  14 __PACKAGE__->config(
  15     default   => 'application/json',
  16     stash_key => 'rest',
  17     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  18     );
  19
  20 sub get_data : Path('/ajax/breeder/search') Args(0) {
  21   my $self = shift;
  22   my $c = shift;
  23   my $j = JSON::Any->new;
  24
  25   my @criteria_list = $c->req->param('categories[]');
  26   my @querytypes = $c->req->param('querytypes[]');
  27
  28   #print STDERR "criteria list = " . Dumper(@criteria_list);
  29   #print STDERR "querytypes = " . Dumper(@querytypes);
  30
  31   my $dataref = {};
  32   my $queryref = {};
  33
  34   my $error = '';
  35
  36   print STDERR "Validating criteria_list\n";
  37   foreach my $select (@criteria_list) { #ensure criteria list arguments are one of the possible categories
  38     chomp($select);
  39     if (! any { $select eq $_ } ('accessions', 'breeding_programs', 'genotyping_protocols', 'locations', 'plants', 'plots', 'seedlots', 'trait_components', 'traits', 'trials', 'trial_designs', 'trial_types', 'years', undef)) {
  40       $error = "Valid keys are accessions, breeding_programs, genotyping_protocols, locations, plants, plots, seedlots, trait_components, traits, trials, trial_designs, trial_types and years or undef";
  41       $c->stash->{rest} = { error => $error };
  42       return;
  43     }
  44   }
  45
  46   print STDERR "Validating query types\n";
  47   foreach my $binary_number (@querytypes) {# ensure querytype arguments are 0 or 1
  48     chomp($binary_number);
  49     if (! any { $binary_number == $_ } ( 0 , 1 )) {
  50       $error = "Valid querytypes are '1' for intersect or '0' for union";
  51       $c->stash->{rest} = { error => $error };
  52       return;
  53     }
  54   }
  55
  56   my $criteria_list = \@criteria_list;
  57   for (my $i=0; $i<scalar(@$criteria_list); $i++) {
  58     my @data;
  59     my $param = $c->req->param("data[$i][]");
  60     if (defined($param) && ($param ne '')) { @data =  $c->req->param("data[$i][]"); }
  61
  62     if (@data) {
  63       print STDERR "Validating dataref ids\n";
  64       for (my $i=0; $i<@data; $i++) { # ensure dataref arguements (ids) are numeric
  65         if (m/\D/) {
  66           $error = "Valid values for dataref are numeric ids";
  67           $c->stash->{rest} = { error => $error };
  68           return;
  69         }
  70       }
  71       my @cdata = map {"'$_'"} @data;
  72       my $qdata = join ",", @cdata;
  73       $dataref->{$criteria_list->[-1]}->{$criteria_list->[$i]} = $qdata;
  74       $queryref->{$criteria_list->[-1]}->{$criteria_list->[$i]} = $querytypes[$i];
  75     }
  76   }
  77
  78   my $dbh = $c->dbc->dbh();
  79   my $bs = CXGN::BreederSearch->new( { dbh=>$dbh } );
  80   my $status = $bs->test_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass});
  81   if ($status->{'error'}) {
  82       $c->stash->{rest} = { error => $status->{'error'}};
  83       return;
  84   }
  85   my $results_ref = $bs->metadata_query(\@criteria_list, $dataref, $queryref);
  86
  87   print STDERR "RESULTS: ".Data::Dumper::Dumper($results_ref);
  88   my @results =@{$results_ref->{results}};
  89
  90
  91   if (@results >= 100_000) {
  92     $c->stash->{rest} = { list => [], message => scalar(@results).' matches. This is too many to display, please narrow your search' };
  93     return;
  94   }
  95   elsif (@results >= 10_000) {
  96     $c->stash->{rest} = { list => \@results, message => 'Over 10,000 matches. Speeds may be affected, consider narrowing your search' };
  97     return;
  98   }
  99   elsif (@results < 1) {
 100     $c->stash->{rest} = { list => \@results, message => scalar(@results).' matches. Nothing to display' };
 101     return;
 102   }
 103   else {
 104     $c->stash->{rest} = { list => \@results };
 105     return;
 106   }
 107
 108 }
 109
 110 sub get_avg_phenotypes : Path('/ajax/breeder/search/avg_phenotypes') Args(0) {
 111   my $self = shift;
 112   my $c = shift;
 113
 114   my $trial_id = $c->req->param('trial_id');
 115   my @trait_ids = $c->req->param('trait_ids[]');
 116   my @weights = $c->req->param('coefficients[]');
 117   my @controls = $c->req->param('controls[]');
 118   my $allow_missing = $c->req->param('allow_missing');
 119
 120   my $dbh = $c->dbc->dbh();
 121   my $bs = CXGN::BreederSearch->new( { dbh=>$dbh } );
 122
 123   my $results_ref = $bs->avg_phenotypes_query($trial_id, \@trait_ids, \@weights, \@controls, $allow_missing);
 124
 125   $c->stash->{rest} = {
 126     error => $results_ref->{'error'},
 127     raw_avg_values => $results_ref->{'raw_avg_values'},
 128     weighted_values => $results_ref->{'weighted_values'}
 129   };
 130
 131   return;
 132
 133 }
 134
 135 sub refresh_matviews : Path('/ajax/breeder/refresh') Args(0) {
 136   my $self = shift;
 137   my $c = shift;
 138
 139   print STDERR "dbname=" . $c->config->{dbname} ."\n";
 140
 141   my $dbh = $c->dbc->dbh();
 142   my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
 143   my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass});
 144
 145   if ($refresh->{error}) {
 146     print STDERR "Returning with error . . .\n";
 147     $c->stash->{rest} = { error => $refresh->{'error'} };
 148     return;
 149   }
 150   else {
 151     $c->stash->{rest} = { message => $refresh->{'message'} };
 152     return;
 153   }
 154 }
 155
 156 sub check_status : Path('/ajax/breeder/check_status') Args(0) {
 157   my $self = shift;
 158   my $c = shift;
 159
 160   my $dbh = $c->dbc->dbh();
 161
 162   my $bs = CXGN::BreederSearch->new( { dbh=>$dbh } );
 163   my $status = $bs->matviews_status();
 164
 165   if ($status->{refreshing}) {
 166     $c->stash->{rest} = { refreshing => $status->{'refreshing'} };
 167     return;
 168   }
 169   else {
 170     $c->stash->{rest} = { timestamp => $status->{'timestamp'} };
 171     return;
 172   }
 173 }