lib/SGN/Controller/AJAX/Genefamily/Manual.pm

   1 =head1 NAME
   2
   3 SGN::Controller::AJAX::Genefamily::Manual - a REST controller class to provide the
   4 backend for objects linked with manual curated gene family (a phenome locusgroup)
   5
   6 =head1 DESCRIPTION
   7
   8 Add new locus members to an existing gene family
   9
  10 =head1 AUTHOR
  11
  12 Naama Menda <nm249@cornell.edu>
  13
  14
  15 =cut
  16
  17 package SGN::Controller::AJAX::Genefamily::Manual;
  18
  19 use Moose;
  20
  21 use List::MoreUtils qw /any /;
  22 use Try::Tiny;
  23 use CXGN::Phenome::Schema;
  24 use CXGN::Chado::Publication;
  25
  26 use CXGN::Page::FormattingHelpers qw/ info_table_html html_alternate_show /;
  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
  37 sub display_locusgroup_members : Chained('/genefamily/manual/get_genefamily') :PathPart('members') : ActionClass('REST') { }
  38
  39 sub display_locusgroup_members_GET  {
  40     my ($self, $c) = @_;
  41     my $html;
  42     my %data;
  43     my $locusgroup = $c->stash->{genefamily};
  44     my $members = $locusgroup->get_cxgn_members;
  45     foreach my $locus_id (keys %$members) {
  46         my $locus = $members->{$locus_id}->{locus};
  47         my $locus_name = $locus->get_locus_name;
  48         my $common_name = $locus->get_common_name;
  49         my $evidence = $members->{$locus_id}->{evidence};
  50         my $ref = $members->{$locus_id}->{reference};
  51         no warnings 'uninitialized';
  52         $data{$common_name} .= qq|<a href="/locus/$locus_id/view">$locus_name</a> ($evidence. $ref)<br />| ;
  53     }
  54     foreach my $common_name (sort keys %data) {
  55         $html .= info_table_html( $common_name  => $data{$common_name},
  56                                   '__border'   => 0, );
  57     }
  58     my $hashref;
  59     $hashref->{html} = $html;
  60     $c->stash->{rest} = $hashref;
  61 }
  62
  63
  64 sub add_member:Path('/ajax/genefamily/manual/add') :ActionClass('REST') {}
  65
  66 sub add_member_GET :Args(0) {
  67     my ($self, $c) = @_;
  68     $c->stash->{rest} = { error => "Nothing here, it's a GET.." } ;
  69 }
  70
  71 sub add_member_POST :Args(0) {
  72     my ( $self, $c ) = @_;
  73     my $locusgroup_id = $c->req->param('locusgroup_id');
  74     my $locus_input   = $c->req->param('locus') ;
  75     my $evidence_id   = $c->req->param('evidence_id') ;
  76     my $reference_id  = $c->req->param('reference_id') ||
  77         CXGN::Chado::Publication::get_curator_ref($c->dbc->dbh);
  78     if (!$locus_input) {
  79         $self->status_bad_request($c, message => 'need locus input param' );
  80         return;
  81     }
  82     my ($locus_name, $locus_symbol, $locus_id) = split (/\|/ ,$locus_input);
  83     my $phenome_schema = $c->dbic_schema('CXGN::Phenome::Schema');
  84     my $locus = $phenome_schema
  85         ->resultset('Locus')
  86         ->find({ locus_id => $locus_id, {} } );
  87     if (!$locus) {
  88         $c->stash->{rest} = { error => "no locus found for id '$locus_id' " };
  89         return;
  90     }
  91     my $locusgroup = $phenome_schema->resultset("Locusgroup")->find({locusgroup_id => $locusgroup_id } ) ;
  92     if (!$c->user) {
  93         $c->stash->{rest} = { error => 'Must be logged in for associating loci! ' };
  94         return;
  95     }
  96     if ( any { $_ eq 'curator' || $_ eq 'submitter' || $_ eq 'sequencer' } $c->user->roles() ) {
  97         # if this fails, it will throw an acception and will (probably rightly) be counted as a server error
  98         my $user_id = $c->user->get_object->get_sp_person_id;
  99         if ($locusgroup && $locus_id) {
 100             try {
 101                 my $locusgroup_member = $phenome_schema->resultset("LocusgroupMember")->find_or_create( {
 102                     locusgroup_id => $locusgroup_id,
 103                     locus_id      => $locus_id,
 104                     sp_person_id  => $user_id,
 105                     evidence_id   => $evidence_id,
 106                     reference_id  => $reference_id,
 107                                                                                                         });
 108                 $c->stash->{rest} = ['success'];
 109                 # need to update the loci div!!
 110                 return;
 111             } catch {
 112                 $c->stash->{rest} = { error => "Failed: $_" };
 113                 return;
 114             };
 115         } else {
 116             $c->stash->{rest} = { error => 'need both valid locusgroup_id and locus_id for adding the locusgroup member! ' };
 117         }
 118     } else {
 119         $c->stash->{rest} = { error => 'No privileges for adding new locus to the locusgroup. You must have an sgn submitter account. Please contact sgn-feedback@solgenomics.net for upgrading your user account. ' };
 120     }
 121 }
 122
 123
 124 1;