lib/SGN/Controller/AJAX/Accessions.pm

   1
   2 =head1 NAME
   3
   4 SGN::Controller::AJAX::Accessions - a REST controller class to provide the
   5 backend for managing accessions
   6
   7 =head1 DESCRIPTION
   8
   9 Managing accessions
  10
  11 =head1 AUTHOR
  12
  13 Jeremy Edwards <jde22@cornell.edu>
  14
  15 =cut
  16
  17 package SGN::Controller::AJAX::Accessions;
  18
  19 use Moose;
  20 use JSON -support_by_pp;
  21 use List::MoreUtils qw /any /;
  22 use CXGN::BreedersToolbox::Accessions;
  23 use CXGN::BreedersToolbox::AccessionsFuzzySearch;
  24 use CXGN::Stock::AddStocks;
  25 use Data::Dumper;
  26 #use JSON;
  27
  28 BEGIN { extends 'Catalyst::Controller::REST' }
  29
  30 __PACKAGE__->config(
  31     default   => 'application/json',
  32     stash_key => 'rest',
  33     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  34    );
  35
  36 sub verify_accession_list : Path('/ajax/accession_list/verify') : ActionClass('REST') { }
  37
  38 sub verify_accession_list_GET : Args(0) {
  39     my $self = shift;
  40     my $c = shift;
  41     $self->verify_accession_list_POST($c);
  42 }
  43
  44 sub verify_accession_list_POST : Args(0) {
  45   my ($self, $c) = @_;
  46
  47   my $accession_list_json = $c->req->param('accession_list');
  48   my @accession_list = @{_parse_list_from_json($accession_list_json)};
  49
  50   my $do_fuzzy_search = $c->req->param('do_fuzzy_search');
  51
  52   if ($do_fuzzy_search) {
  53       $self->do_fuzzy_search($c, \@accession_list);
  54   }
  55   else {
  56       $self->do_exact_search($c, \@accession_list);
  57   }
  58
  59 }
  60
  61 sub do_fuzzy_search {
  62     my $self = shift;
  63     my $c = shift;
  64     my $accession_list = shift;
  65
  66     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  67     my $fuzzy_accession_search = CXGN::BreedersToolbox::AccessionsFuzzySearch->new({schema => $schema});
  68     my $fuzzy_search_result;
  69     my $max_distance = 0.2;
  70     my @accession_list = @$accession_list;
  71     my @found_accessions;
  72     my @fuzzy_accessions;
  73     my @absent_accessions;
  74
  75     if (!$c->user()) {
  76         $c->stash->{rest} = {error => "You need to be logged in to add accessions." };
  77         return;
  78     }
  79     if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)  ) {
  80         $c->stash->{rest} = {error =>  "You have insufficient privileges to add accessions." };
  81         return;
  82     }
  83
  84     $fuzzy_search_result = $fuzzy_accession_search->get_matches(\@accession_list, $max_distance);
  85     print STDERR "\n\nResult:\n".Data::Dumper::Dumper($fuzzy_search_result)."\n\n";
  86
  87     @found_accessions = $fuzzy_search_result->{'found'};
  88     @fuzzy_accessions = $fuzzy_search_result->{'fuzzy'};
  89     @absent_accessions = $fuzzy_search_result->{'absent'};
  90
  91     $c->stash->{rest} = {
  92         success => "1",
  93         absent => @absent_accessions,
  94         fuzzy => @fuzzy_accessions,
  95         found => @found_accessions
  96     };
  97     return;
  98 }
  99
 100 sub do_exact_search {
 101     my $self = shift;
 102     my $c = shift;
 103     my $accession_list = shift;
 104
 105     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 106
 107     my @found_accessions;
 108     my @absent_accessions;
 109     my @fuzzy_accessions;
 110
 111     foreach my $a (@$accession_list) {
 112         print STDERR "CHECKING $a...\n";
 113         my $exact_search_rs = $schema->resultset("Stock::Stock")->search( { -or => { name => { -ilike => $a}, uniquename => { -ilike => $a }}});
 114         if ($exact_search_rs->count() > 0) {
 115             push @found_accessions, { unique_name => $a, matched_string => $a };
 116         }
 117         else {
 118             my $exact_synonym_rs = $schema->resultset("Stock::Stockprop")->search(
 119                 { value =>
 120                   {
 121                       -ilike => $a },
 122                   'lower(type.name)' => { like => '%synonym%' },
 123                 },
 124                 {join => 'type' }
 125                 );
 126             if ($exact_synonym_rs ->count() > 0) {
 127                 push @found_accessions, { unique_name => $a,  matched_string => $a};
 128                 push @fuzzy_accessions, { unique_name => $a,  matched_string => $a};
 129             }
 130             else {
 131                 push @absent_accessions, $a;
 132             }
 133         }
 134     }
 135
 136     my $rest = {
 137         success => "1",
 138         absent => \@absent_accessions,
 139         found => \@found_accessions,
 140         fuzzy => \@fuzzy_accessions
 141     };
 142     print STDERR Dumper($rest);
 143     $c->stash->{rest} = $rest;
 144 }
 145
 146 sub add_accession_list : Path('/ajax/accession_list/add') : ActionClass('REST') { }
 147
 148 sub add_accession_list_POST : Args(0) {
 149   my ($self, $c) = @_;
 150   my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 151   my $accession_list_json = $c->req->param('accession_list');
 152   my $species_name = $c->req->param('species_name');
 153   my $population_name = $c->req->param('population_name');
 154   my @accession_list;
 155   my $stock_add;
 156   my $validated;
 157   my $added;
 158   my $dbh = $c->dbc->dbh;
 159   my $user_id;
 160   my $owner_name;
 161   my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 162
 163   if (!$c->user()) {
 164     $c->stash->{rest} = {error => "You need to be logged in to create a field book" };
 165     return;
 166   }
 167
 168   $user_id = $c->user()->get_object()->get_sp_person_id();
 169   $owner_name = $c->user()->get_object()->get_username();
 170
 171   if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)  ) {
 172     $c->stash->{rest} = {error =>  "You have insufficient privileges to create a field book." };
 173     return;
 174   }
 175
 176   @accession_list = @{_parse_list_from_json($accession_list_json)};
 177   if ($population_name eq '') {
 178       $stock_add = CXGN::Stock::AddStocks->new({ schema => $schema, stocks => \@accession_list, species => $species_name, owner_name => $owner_name,phenome_schema => $phenome_schema, dbh => $dbh} );
 179   } else {
 180       $stock_add = CXGN::Stock::AddStocks->new({ schema => $schema, stocks => \@accession_list, species => $species_name, owner_name => $owner_name,phenome_schema => $phenome_schema, dbh => $dbh, population_name => $population_name} );
 181   }
 182   $validated = $stock_add->validate_stocks();
 183   if (!$validated) {
 184     $c->stash->{rest} = {error =>  "Stocks already exist in the database" };
 185   }
 186   $added = $stock_add->add_accessions();
 187   if (!$added) {
 188     $c->stash->{rest} = {error =>  "Could not add stocks to the database" };
 189   }
 190   $c->stash->{rest} = {success => "1"};
 191   return;
 192 }
 193
 194 sub populations : Path('/ajax/manage_accessions/populations') : ActionClass('REST') { }
 195
 196 sub populations_GET : Args(0) {
 197     my $self = shift;
 198     my $c = shift;
 199
 200     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 201     my $ac = CXGN::BreedersToolbox::Accessions->new( { schema=>$schema });
 202     my $populations = $ac->get_all_populations($c);
 203
 204     $c->stash->{rest} = { populations => $populations };
 205 }
 206
 207 sub _parse_list_from_json {
 208   my $list_json = shift;
 209   my $json = new JSON;
 210   if ($list_json) {
 211     my $decoded_list = $json->allow_nonref->utf8->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($list_json);
 212     #my $decoded_list = decode_json($list_json);
 213     my @array_of_list_items = @{$decoded_list};
 214     return \@array_of_list_items;
 215   }
 216   else {
 217     return;
 218   }
 219 }
 220
 221
 222 1;