lib/SGN/Controller/Stock.pm

   1 package SGN::Controller::Stock;
   2
   3 =head1 NAME
   4
   5 SGN::Controller::Stock - Catalyst controller for pages dealing with stocks (e.g. accession, poopulation, etc.)
   6
   7 =cut
   8
   9 use Moose;
  10 use namespace::autoclean;
  11
  12 use URI::FromHash 'uri';
  13
  14 use CXGN::Chado::Stock;
  15 use SGN::View::Stock qw/stock_link stock_organisms stock_types/;
  16
  17 has 'schema' => (
  18     is       => 'rw',
  19     isa      => 'DBIx::Class::Schema',
  20     required => 0,
  21 );
  22
  23 has 'default_page_size' => (
  24     is      => 'ro',
  25     default => 20,
  26 );
  27
  28
  29 BEGIN { extends 'Catalyst::Controller' }
  30 with 'Catalyst::Component::ApplicationAttribute';
  31
  32 sub _validate_pair {
  33     my ($self,$c,$key,$value) = @_;
  34     $c->throw( is_client_error => 1, public_message => "$value is not a valid value for $key" )
  35         if ($key =~ m/_id$/ and $value !~ m/\d+/);
  36 }
  37
  38 sub search :Path('/stock/search') Args(0) {
  39     my ( $self, $c ) = @_;
  40     $self->schema( $c->dbic_schema('Bio::Chado::Schema','sgn_chado') );
  41
  42     my $req = $c->req;
  43
  44     my $results;
  45     $results = $self->_make_stock_search_rs( $c, $req ) if $req->param('submit');
  46
  47     $c->stash(
  48         template => '/stock/search.mas',
  49         request => $req,
  50         form_opts    => { stock_types=>stock_types($self->schema), organisms=>stock_organisms($self->schema)} ,
  51         results  => $results,
  52         sp_person_autocomplete_uri => $c->uri_for( '/ajax/people/autocomplete' ),
  53         pagination_link_maker => sub {
  54             return uri( query => { %{$req}, page => shift } );
  55         },
  56     );
  57 }
  58
  59
  60 # assembles a DBIC resultset for the search based on the submitted
  61 # form values
  62 sub _make_stock_search_rs {
  63     my ( $self, $c, $req ) = @_;
  64
  65     my $rs = $self->schema->resultset('Stock::Stock');
  66     my $rs_synonyms;
  67
  68     if( my $name = $req->param('stock_name') ) {
  69         $rs = $rs->search({
  70             -or => [
  71                  'lower(me.name)' => { like => '%'.lc( $name ).'%' } ,
  72                  'lower(uniquename)' => { like => '%'.lc( $name ).'%' },
  73               #   -and => [
  74               #       'lower(type.name)' => { like =>'%synonym%' },
  75               #       'lower(value)' => { like =>'%'.lc( $name ).'%' },
  76               #   ],
  77               #  ], },
  78               #            {  join => { 'stockprops' => 'type' } },
  79                 ], } ,
  80             );
  81         #add the stockprop values here
  82         $rs_synonyms =  $self->schema->resultset('Cv::Cvterm')->search( {
  83             'lower(me.name)' => { like =>'%synonym%' } , } )->search_related('stockprops', {
  84                 'lower(value)' => { like =>'%'.lc( $name ).'%' } , } )->
  85                     search_related('stock');
  86
  87     }
  88     if( my $type = $req->param('stock_type') ) {
  89         $self->_validate_pair($c,'type_id',$type);
  90         $rs = $rs->search({ 'type_id' => $type });
  91     }
  92
  93     if( my $organism = $req->param('organism') ) {
  94         $self->_validate_pair( $c, 'organism_id', $organism );
  95         $rs = $rs->search({ 'organism_id' => $organism });
  96     }
  97
  98     if ( my $editor = $req->param('person') ) {
  99         print STDERR "Searching stock by editor | $editor | ***********\n\n";
 100         $self->_validate_pair( $c, 'person') ;
 101         my ($first_name, $last_name) = split ',' , $editor ;
 102         $first_name  =~ s/\s//g;
 103         $last_name  =~ s/\s//g;
 104         print STDERR "first_name = |$first_name| , last_name = |$last_name| ***********\n\n";
 105         my $q = "SELECT stock_id  FROM stock
 106                  JOIN stockprop USING (stock_id)
 107                  JOIN sgn_people.sp_person on cast(value AS numeric) = sp_person_id
 108                  JOIN cvterm on stockprop.type_id = cvterm_id
 109                  WHERE first_name = ? AND last_name = ?
 110                  AND cvterm.name = ?";
 111         my $sth = $c->dbc->dbh->prepare($q);
 112         $sth->execute($first_name, $last_name, 'sp_person_id');
 113
 114         my $query = "SELECT sp_person_id FROM sgn_people.sp_person
 115                      WHERE first_name = ? AND last_name = ?";
 116         $sth = $c->dbc->dbh->prepare($query);
 117         $sth->execute($first_name, $last_name);
 118         my ($sp_person_id) = $sth->fetchrow_array ;
 119         print STDERR "SP_PERSON_ID = $sp_person_id *********\n\n";
 120         $rs = $rs->search( {
 121             'type.name' => 'sp_person_id',
 122             'stockprops.value' => $sp_person_id, } ,
 123                            { join => { stockprops =>['type'] } },
 124             ) if $sp_person_id;
 125     }
 126     # page number and page size, and order by name
 127     $rs = $rs->search( undef, {
 128         page => $req->param('page')      || 1,
 129         rows => $req->param('page_size') || $self->default_page_size,
 130         order_by => 'name',
 131                        });
 132     return $rs;
 133 }
 134
 135
 136 # sub view_id :Path('/stock/view/id') :Args(1) {
 137 #     my ( $self, $c , $stock_id) = @_;
 138
 139 #     $self->schema( $c->dbic_schema( 'Bio::Chado::Schema', 'sgn_chado' ) );
 140 #     $self->_view_stock($c, 'view', $stock_id);
 141 # }
 142
 143
 144 sub new_stock :Chained('get_stock') : PathPart('new') :Args(0) {
 145     my ( $self, $c ) = @_;
 146    # $self->schema( $c->dbic_schema( 'Bio::Chado::Schema', 'sgn_chado' ) );
 147   ####  $c->forward("view_stock", 'new');
 148     $c->stash(
 149         template => '/stock/index.mas',
 150
 151         stockref => {
 152             action    => "new",
 153             stock_id  => 0 ,
 154             #curator   => $curator,
 155             #submitter => $submitter,
 156             #sequencer => $sequencer,
 157             #person_id => $person_id,
 158             stock     => $c->stash->{stock},
 159             schema    => $self->schema,
 160             #dbh       => $dbh,
 161             #is_owner  => $is_owner,
 162             #props     => $props,
 163             #dbxrefs   => $dbxrefs,
 164             #owners    => $owner_ids,
 165         },
 166         );
 167 }
 168
 169
 170 sub view_stock :Chained('get_stock') :PathPart('view') :Args(0) {
 171     my ( $self, $c, $action) = @_;
 172     my $logged_user = $c->user;
 173     my $person_id = $logged_user->get_object->get_sp_person_id if $logged_user;
 174     my $curator = $logged_user->check_roles('curator') if $logged_user;
 175     my $submitter = $logged_user->check_roles('submitter') if $logged_user;
 176     my $sequencer = $logged_user->check_roles('sequencer') if $logged_user;
 177
 178     my $dbh = $c->dbc->dbh;
 179
 180     ##################
 181
 182     ###Check if a stock page can be printed###
 183
 184     my $stock = $c->stash->{stock};
 185     my $stock_id = $stock ? $stock->get_stock_id : undef ;
 186
 187     # print message if stock_id is not valid
 188     unless ( ( $stock_id =~ m /^\d+$/ ) || ($action eq 'new' && !$stock_id) ) {
 189         $c->throw_404( "No stock/accession exists for identifier $stock_id" );
 190     }
 191     if (  !$stock->get_object_row  || ($action ne 'new' && !$stock_id) ) {
 192         $c->throw_404( "No stock/accession exists for identifier $stock_id" );
 193     }
 194
 195     # print message if the stock is obsolete
 196     my $obsolete = $stock->get_is_obsolete();
 197     if ( $obsolete  && !$curator ) {
 198         $c->throw(is_client_error => 0,
 199                   title             => 'Obsolete stock',
 200                   message           => "Stock $stock_id is obsolete!",
 201                   developer_message => 'only curators can see obsolete stock',
 202                   notify            => 0,   #< does not send an error email
 203             );
 204     }
 205     # print message if stock_id does not exist
 206     if ( !$stock && $action ne 'new' && $action ne 'store' ) {
 207         $c->throw_404('No stock exists for this identifier');
 208     }
 209
 210     ####################
 211     my $props = $self->_stockprops($stock);
 212     my $is_owner;
 213     my $owner_ids = $props->{sp_person_id} || [] ;
 214     if ( $stock && ($curator || $person_id && ( grep /^$person_id$/, @$owner_ids ) ) ) {
 215         $is_owner = 1;
 216     }
 217     my $dbxrefs = $self->_stock_dbxrefs($stock);
 218
 219     ################
 220     $c->stash(
 221         template => '/stock/index.mas',
 222
 223         stockref => {
 224             action    => $action,
 225             stock_id  => $stock_id ,
 226             curator   => $curator,
 227             submitter => $submitter,
 228             sequencer => $sequencer,
 229             person_id => $person_id,
 230             stock     => $stock,
 231             schema    => $self->schema,
 232             dbh       => $dbh,
 233             is_owner  => $is_owner,
 234             props     => $props,
 235             dbxrefs   => $dbxrefs,
 236             owners    => $owner_ids,
 237         },
 238         locus_add_uri  => $c->uri_for( '/ajax/stock/associate_locus' ),
 239         locus_autocomplete_uri => $c->uri_for( '/ajax/locus/autocomplete' ),
 240
 241         );
 242 }
 243
 244 sub _stockprops {
 245     my ($self,$stock) = @_;
 246
 247
 248     my $stockprops = $stock->get_object_row()->search_related("stockprops");
 249
 250     my $properties ;
 251     while ( my $prop =  $stockprops->next ) {
 252         push @{ $properties->{$prop->type->name} } ,   $prop->value ;
 253     }
 254     return $properties;
 255 }
 256
 257
 258 sub _stock_dbxrefs {
 259     my ($self,$stock) = @_;
 260
 261     my $stock_dbxrefs = $stock->get_object_row()->search_related("stock_dbxrefs");
 262
 263     my $dbxrefs ;
 264     while ( my $sdbxref =  $stock_dbxrefs->next ) {
 265         my $url = $sdbxref->dbxref->db->urlprefix . $sdbxref->dbxref->db->url;
 266
 267         my $accession = $sdbxref->dbxref->accession;
 268         $url = $url ? qq |<a href = "$url/$accession">$accession</a>| : $accession ;
 269         push @{ $dbxrefs->{$sdbxref->dbxref->db->name} } , $accession ;
 270     }
 271     return $dbxrefs;
 272 }
 273
 274 sub get_stock :Chained('/') :PathPart('stock') :CaptureArgs(1) {
 275     my ($self, $c, $stock_id) = @_;
 276
 277     $self->schema( $c->dbic_schema( 'Bio::Chado::Schema', 'sgn_chado' ) );
 278     $c->stash->{stock} = CXGN::Chado::Stock->new($self->schema, $stock_id);
 279
 280     #add the stockprops to the stash
 281     my $stock = $c->stash->{stock}->get_object_row;
 282     my $stockprops = $stock ? $stock->search_related("stockprops") : undef ;
 283
 284     my $properties ;
 285     if ($stockprops) {
 286         while ( my $prop =  $stockprops->next ) {
 287             push @{ $properties->{$prop->type->name} } ,   $prop->value ;
 288         }
 289     }
 290     $c->stash->{stockprops} = $properties;
 291
 292 }
 293
 294
 295 ######
 296 1;
 297 ######