cgi-bin/jsforms/locusgroup_ajax_form.pl

   1
   2 use strict;
   3 use warnings;
   4
   5 my $form = CXGN::Phenome::LocusGroupForm->new();
   6
   7 package CXGN::Phenome::LocusGroupForm;
   8
   9 use base qw/CXGN::Page::Form::AjaxFormPage  /;
  10
  11 use CXGN::Phenome::LocusGroup;
  12 use CXGN::Phenome::Schema;
  13
  14 use CXGN::Tools::Organism;
  15
  16 use CXGN::People::Person;
  17 use CXGN::Contact;
  18 use CXGN::Feed;
  19
  20 use Try::Tiny;
  21
  22 use JSON;
  23
  24
  25 sub new {
  26     my $class  = shift;
  27     my $self   = $class->SUPER::new(@_);
  28     return $self;
  29 }
  30
  31 sub define_object {
  32     my $self = shift;
  33     my %args      = $self->get_args();
  34     my $lg_id  = $args{locusgroup_id} || $args{object_id};
  35     my $user_type = $self->get_user()->get_user_type();
  36     my %json_hash= $self->get_json_hash();
  37     my $schema= CXGN::Phenome::Schema->connect( sub { $self->get_dbh->get_actual_dbh } , { on_connect_do => ['set search_path to public,phenome;'] }  );
  38
  39     $self->set_object_id($lg_id);
  40     $self->set_object_name('LocusGroup'); #this is useful for email messages
  41     $self->set_object(
  42         CXGN::Phenome::LocusGroup->new( $schema, $self->get_object_id ) );
  43     if ( $self->get_object()->get_obsolete() eq 't' && $user_type ne 'curator' )
  44     {
  45         $json_hash{error}="Locus group $lg_id is obsolete!";
  46     }
  47     unless ( ( $lg_id =~ m /^\d+$/ || !$lg_id  )  ) {
  48         $json_hash{error}="No locus group exists for identifier $lg_id";
  49     }
  50     $self->set_json_hash(%json_hash);
  51     $self->set_primary_key("locusgroup_id");
  52     $self->set_owners( $self->get_object->get_sp_person_id );
  53     $self->print_json() if $json_hash{error};
  54 }
  55
  56
  57 sub store {
  58     my $self=shift;
  59     my $locusgroup    = $self->get_object();
  60     my $lg_id = $self->get_object_id();
  61     my %args     = $self->get_args();
  62     my %json_hash = $self->get_json_hash();
  63     my $initial_lg_id = $lg_id;
  64
  65     my $error;
  66     print STDERR "****locusgroup name arg = " . $args{locusgroup_name} ;
  67     $locusgroup->set_locusgroup_name($args{locusgroup_name});
  68     my ($message) = $locusgroup->exists_in_database($args{locusgroup_name});
  69     my $validate;
  70     if ($message) {
  71         $error = " Locus group $args{locusgroup_name} already exists in the database ";
  72     }else {
  73         try{
  74             $self->SUPER::store(); #this sets $json_hash{validate} if the form validation failed.
  75             $lg_id = $locusgroup->get_locusgroup_id() ;
  76         } catch {
  77             $error = " An error occurred. Cannot store to the database\n An  email message has been sent to the SGN development team";
  78             CXGN::Contact::send_email('locus_ajax_form.pl died', $error . "\n" . $_ , 'sgn-bugs@sgn.cornell.edu');
  79         };
  80     }
  81     #the validate field is false is validation passed for all fields, true if did not pass and the form is re-printed
  82     #$json_hash{validate}= $validate;
  83     %json_hash= $self->get_json_hash();
  84     $validate= $json_hash{validate};
  85     $json_hash{error} = $error if $error;
  86
  87     my $refering_page="/genefamily/manual/$lg_id/view";
  88     $self->send_form_email({subject=>"[New locusgroup details stored] locusgroup $lg_id", mailing_list=>'sgn-db-curation@sgn.cornell.edu', refering_page=>"www.solgenomics.net".$refering_page}) if (!$validate && !$json_hash{error});
  89     $json_hash{refering_page}=$refering_page if !$initial_lg_id && !$validate && !$error;
  90
  91     $self->set_json_hash(%json_hash);
  92     $self->print_json();
  93 }
  94
  95
  96 ####################################
  97 sub delete {
  98     ##Delete the locusgroup (actually set obsolete = 't')
  99     my $self = shift;
 100     my $check = $self->check_modify_privileges();
 101     $self->print_json() if $check ; #error or no user privileges
 102
 103     my $locusgroup = $self->get_object();
 104     my $lg_name = $locusgroup->get_locusgroup_name();
 105     my $lg_id = $locusgroup->get_locusgroup_id();
 106     my %json_hash= $self->get_json_hash();
 107     my $refering_page="/genefamily/manual/$lg_id/view";
 108     if (!$json_hash{error} ) {
 109         try {
 110             $locusgroup->delete();
 111         }catch {
 112             $json_hash{error} = " An error occurred. Cannot delete locusgroup\n An  email message has been sent to the SGN development team";
 113         };
 114         $json_hash{reload} = 1;
 115     }
 116     $self->send_form_email({subject=>"LocusGroup obsoleted ($lg_name)", mailing_list=>'sgn-db-curation@sgn.cornell.edu', refering_page=>"www.solgenomics.net".$refering_page, action=>'delete'}) if (!$json_hash{error});
 117     $self->set_json_hash(%json_hash);
 118     $self->print_json();
 119 }
 120
 121
 122
 123 sub generate_form {
 124     my $self = shift;
 125     my $form_id = 'edit_locusgroup'; # a form_id is required for ajax forms
 126     $self->init_form($form_id) ; ## instantiate static/editable/confirmStore form
 127
 128     my $locusgroup = $self->get_object();
 129     my %args  = $self->get_args();
 130     my $form = $self->get_form();
 131     my $relationship = $locusgroup->get_relationship_name;
 132
 133     if ( $locusgroup->get_obsolete() eq 't' ) {
 134         $form->add_label(
 135             display_name => "Status",
 136             field_name   => "obsolete_stat",
 137             contents     => 'OBSOLETE',
 138             );
 139     }
 140     $form->add_field(
 141         display_name => "Gene family name",
 142         field_name   => "locusgroup_name",
 143         id           => "locusgroup_name",
 144         object       => $locusgroup,
 145         getter       => "get_locusgroup_name",
 146         setter       => "set_locusgroup_name",
 147         validate     => 'string',
 148         );
 149     $form->add_label(
 150         display_name => "Relationship",
 151         field_name   => "relationship",
 152         contents     => $relationship,
 153             );
 154     #$form->add_select(
 155 #       display_name       => "Chromosome ",
 156 #       field_name         => "lg_name",
 157 #       contents           => $locus->get_linkage_group(),
 158 #       length             => 10,
 159 #       object             => $locus,
 160 #       getter             => "get_linkage_group",
 161 #       setter             => "set_linkage_group",
 162         #select_list_ref    => $lg_names_ref,
 163         #select_id_list_ref => $lg_names_ref,
 164 #       );
 165
 166     $form->add_hidden(
 167         field_name => "locusgroup_id",
 168         contents   => $locusgroup->get_locusgroup_id(),
 169         );
 170
 171     $form->add_hidden(
 172         field_name => "action",
 173         contents   => "store",
 174         );
 175
 176     $form->add_hidden(
 177         field_name => "sp_person_id",
 178         contents   => $self->get_user()->get_sp_person_id(),
 179         object     => $locusgroup,
 180         setter     => "set_sp_person_id",
 181
 182         );
 183 #    $form->add_hidden(
 184 #       field_name => "updated_by",
 185 #       contents   => $self->get_user()->get_sp_person_id(),
 186 #       object     => $locusgroup,
 187 #       setter     => "set_updated_by",
 188 #       );
 189
 190     if ( $self->get_action() =~ /view|edit/ ) {
 191         $form->from_database();
 192         #$form->add_hidden(
 193         #    field_name => "common_name_id",
 194         #    contents   => $locus->get_common_name_id(),
 195         #    );
 196     }
 197     elsif ( $self->get_action() =~ /store/ ) {
 198         $form->from_request( %args );
 199     }
 200 }