cgi-bin/jsforms/locus_ajax_form.pl

   1
   2 use strict;
   3 use warnings;
   4
   5 my $locus_form = CXGN::Phenome::LocusForm->new();
   6
   7 package CXGN::Phenome::LocusForm;
   8
   9 use base qw/CXGN::Page::Form::AjaxFormPage  /;
  10
  11 use CXGN::Phenome::Locus;
  12 use CXGN::Phenome::Locus::LinkageGroup;
  13 use CXGN::Tools::Organism;
  14
  15 use CXGN::People::Person;
  16 use CXGN::Contact;
  17 use CXGN::Feed;
  18
  19 use Try::Tiny;
  20
  21 use JSON;
  22
  23
  24 sub new {
  25     my $class  = shift;
  26     my $self   = $class->SUPER::new(@_);
  27 ###    $self->get_ajax_page()->send_http_header();
  28
  29     return $self;
  30 }
  31
  32 sub define_object {
  33     my $self = shift;
  34
  35     my %args      = $self->get_args();
  36     my $locus_id  = $args{locus_id} || $args{object_id};
  37     my $user_type = $self->get_user()->get_user_type();
  38     my %json_hash= $self->get_json_hash();
  39
  40     $self->set_object_id($locus_id);
  41     $self->set_object_name('Locus'); #this is useful for email messages
  42     $self->set_object(
  43         CXGN::Phenome::Locus->new( $self->get_dbh(), $self->get_object_id() ) );
  44     if ( $self->get_object()->get_obsolete() eq 't' && $user_type ne 'curator' )
  45     {
  46         ##print STDERR "ERROR:: Locus $locus_id is obsolete!";
  47         $json_hash{error}="Locus $locus_id is obsolete!";
  48     }
  49     unless ( ( $locus_id =~ m /^\d+$/ || !$locus_id  )  ) {
  50         #print STDERR "ERROR:: 'No locus exists for identifier $locus_id'\n\n";
  51         $json_hash{error}="No locus exists for identifier $locus_id";
  52     }
  53     $self->set_json_hash(%json_hash);
  54     $self->set_primary_key("locus_id");
  55     $self->set_owners( $self->get_object()->get_owners() );
  56
  57     $self->return_json() if $json_hash{error};
  58 }
  59
  60 sub display_form {
  61     my $self = shift;
  62     my %json_hash = $self->get_json_hash();
  63
  64     if (!($json_hash{html}) ) { $json_hash{html} = $self->get_form()->as_table_string() ; }
  65     $self->check_modify_privileges();
  66
  67     $json_hash{"user_type"} = $self->get_user()->get_user_type();
  68     $json_hash{"is_owner"} = $self->get_is_owner();
  69
  70     $json_hash{"editable_form_id"} = $self->get_form()->get_form_id();
  71
  72
  73     $self->set_json_hash(%json_hash);
  74     $self->return_json();
  75 }
  76
  77 sub store {
  78     my $self=shift;
  79
  80     my $locus    = $self->get_object();
  81     my $locus_id = $self->get_object_id();
  82     my %args     = $self->get_args();
  83     my %json_hash = $self->get_json_hash();
  84     my $initial_locus_id = $locus_id;
  85
  86     my $error;
  87     $locus->set_common_name_id($args{common_name_id});
  88
  89     my ($message) =
  90         $locus->exists_in_database( $args{locus_name}, $args{locus_symbol} );
  91     my $validate;
  92     if ($message) {
  93         $error = " Locus $args{locus_name} (symbol=  $args{locus_symbol} ) already exists in the database ";
  94     }else {
  95         try{
  96             $self->SUPER::store(); #this sets $json_hash{validate} if the form validation failed.
  97             $locus_id = $locus->get_locus_id() ;
  98         } catch {
  99             $error = " An error occurred. Cannot store to the database\n An  email message has been sent to the SGN development team";
 100             CXGN::Contact::send_email('locus_ajax_form.pl died', $error . "\n" . $_ , 'sgn-bugs@sgn.cornell.edu');
 101         };
 102     }
 103     #the validate field is false is validation passed for all fields, true if did not pass and the form is re-printed
 104     #$json_hash{validate}= $validate;
 105     %json_hash= $self->get_json_hash();
 106     $validate= $json_hash{validate};
 107     $json_hash{error} = $error if $error;
 108
 109     my $refering_page="/phenome/locus_display.pl?locus_id=$locus_id";
 110     $self->send_form_email({subject=>"[New locus details stored] locus $locus_id", mailing_list=>'sgn-db-curation@sgn.cornell.edu', refering_page=>"www.solgenomics.net".$refering_page}) if (!$validate && !$json_hash{error});
 111     $json_hash{refering_page}=$refering_page if !$initial_locus_id && !$validate && !$error;
 112
 113     $self->set_json_hash(%json_hash);
 114
 115     $self->return_json();
 116 }
 117
 118
 119 ####################################
 120 sub delete {
 121     ##Delete the locus (actually set obsolete = 't')
 122     my $self = shift;
 123     my $check = $self->check_modify_privileges();
 124     $self->return_json() if $check ; #error or no user privileges
 125
 126     my $locus      = $self->get_object();
 127     my $locus_name = $locus->get_locus_name();
 128     my $locus_id = $locus->get_locus_id();
 129     my %json_hash= $self->get_json_hash();
 130     my $refering_page="/phenome/locus_display.pl?locus_id=$locus_id";
 131
 132     if (!$json_hash{error} ) {
 133         try {
 134             $locus->delete();
 135         }catch {
 136             $json_hash{error} = " An error occurred. Cannot delete locus\n An  email message has been sent to the SGN development team";
 137         };
 138         $json_hash{reload} = 1;
 139     }
 140     $self->send_form_email({subject=>"Locus obsoleted ($locus_name)", mailing_list=>'sgn-db-curation@sgn.cornell.edu', refering_page=>"www.solgenomics.net".$refering_page, action=>'delete'}) if (!$json_hash{error});
 141     $self->set_json_hash(%json_hash);
 142     $self->return_json();
 143 }
 144
 145
 146
 147 sub generate_form {
 148     my $self = shift;
 149     my $form_id = 'edit_locus'; # a form_id is required for ajax forms
 150
 151     $self->init_form($form_id) ; ## instantiate static/editable/confirmStore form
 152
 153     my $locus = $self->get_object();
 154     my %args  = $self->get_args();
 155     my $form = $self->get_form();
 156     my $dbh = $self->get_dbh();
 157
 158     my ( $organism_names_ref, $organism_ids_ref ) =
 159         CXGN::Tools::Organism::get_all_organisms( $self->get_dbh() );
 160     my ($lg_names_ref) =
 161         CXGN::Phenome::Locus::LinkageGroup::get_all_lgs( $self->get_dbh() );
 162     my ($lg_arms_ref) =
 163         CXGN::Phenome::Locus::LinkageGroup::get_lg_arms( $self->get_dbh() );
 164
 165     if ( $self->get_action =~ /new|store/ ) {
 166         $self->get_form->add_select(
 167             display_name       => "Organism ",
 168             field_name         => "common_name_id",
 169             contents           => $locus->get_common_name_id(),
 170             length             => 20,
 171             object             => $locus,
 172             getter             => "get_common_name_id",
 173             setter             => "set_common_name_id",
 174             select_list_ref    => $organism_names_ref,
 175             select_id_list_ref => $organism_ids_ref,
 176             );
 177
 178     }
 179     if ( $locus->get_obsolete() eq 't' ) {
 180         $form->add_label(
 181             display_name => "Status",
 182             field_name   => "obsolete_stat",
 183             contents     => 'OBSOLETE',
 184             );
 185     }
 186     $form->add_field(
 187         display_name => "Locus name ",
 188         field_name   => "locus_name",
 189         object       => $locus,
 190         getter       => "get_locus_name",
 191         setter       => "set_locus_name",
 192         validate     => 'string',
 193         );
 194
 195     $form->add_field(
 196         display_name => "Symbol ",
 197         field_name   => "locus_symbol",
 198         object       => $locus,
 199         getter       => "get_locus_symbol",
 200         setter       => "set_locus_symbol",
 201         validate     => 'token',
 202         formatting   => '<i>*</i>',
 203         );
 204
 205     $form->add_field(
 206         display_name => "Gene activity ",
 207         field_name   => "gene_activity",
 208         object       => $locus,
 209         getter       => "get_gene_activity",
 210         setter       => "set_gene_activity",
 211         length       => '50',
 212         );
 213
 214     $form->add_textarea(
 215         display_name => "Description ",
 216         field_name   => "description",
 217         object       => $locus,
 218         getter       => "get_description",
 219         setter       => "set_description",
 220         columns      => 40,
 221         rows         => => 4,
 222         );
 223
 224     $form->add_select(
 225         display_name       => "Chromosome ",
 226         field_name         => "lg_name",
 227         contents           => $locus->get_linkage_group(),
 228         length             => 10,
 229         object             => $locus,
 230         getter             => "get_linkage_group",
 231         setter             => "set_linkage_group",
 232         select_list_ref    => $lg_names_ref,
 233         select_id_list_ref => $lg_names_ref,
 234         );
 235
 236     $form->add_select(
 237         display_name       => "Arm",
 238         field_name         => "lg_arm",
 239         contents           => $locus->get_lg_arm(),
 240         length             => 10,
 241         object             => $locus,
 242         getter             => "get_lg_arm",
 243         setter             => "set_lg_arm",
 244         select_list_ref    => $lg_arms_ref,
 245         select_id_list_ref => $lg_arms_ref,
 246         );
 247
 248     $form->add_hidden(
 249         field_name => "locus_id",
 250         contents   => $locus->get_locus_id(),
 251         );
 252
 253     $form->add_hidden(
 254         field_name => "action",
 255         contents   => "store",
 256         );
 257
 258     $form->add_hidden(
 259         field_name => "sp_person_id",
 260         contents   => $self->get_user()->get_sp_person_id(),
 261         object     => $locus,
 262         setter     => "set_sp_person_id",
 263
 264         );
 265     $form->add_hidden(
 266         field_name => "updated_by",
 267         contents   => $self->get_user()->get_sp_person_id(),
 268         object     => $locus,
 269         setter     => "set_updated_by",
 270         );
 271
 272     if ( $self->get_action() =~ /view|edit/ ) {
 273         $form->from_database();
 274         $form->add_hidden(
 275             field_name => "common_name_id",
 276             contents   => $locus->get_common_name_id(),
 277             );
 278
 279     }
 280     elsif ( $self->get_action() =~ /store/ ) {
 281         $form->from_request( %args );
 282     }
 283 }
 284
 285
 286