lib/CXGN/Phenome.pm

   1 package CXGN::Phenome;
   2 use strict;
   3 use warnings;
   4
   5 ####################
   6
   7 use base qw/CXGN::Search::DBI::Simple CXGN::Search::WWWSearch/;
   8
   9 __PACKAGE__->creates_result('CXGN::Phenome::Result');
  10 __PACKAGE__->uses_query('CXGN::Phenome::Query');
  11
  12 #####################
  13
  14 package CXGN::Phenome::Result;
  15 use base qw/CXGN::Search::BasicResult/;
  16
  17 #####################
  18
  19 package CXGN::Phenome::Query;
  20 use CXGN::Page::FormattingHelpers
  21   qw(
  22      simple_selectbox_html
  23      info_table_html
  24      hierarchical_selectboxes_html
  25      conditional_like_input_html
  26      html_optional_show
  27     );
  28
  29 use CXGN::Tools::Organism;
  30 use CXGN::Phenome::Locus::LinkageGroup;
  31 use base qw/CXGN::Search::DBI::Simple::WWWQuery/;
  32 our %pname;
  33
  34 sub _cached_dbh() { our $_cached_dbc ||= CXGN::DB::Connection->new }
  35 my $phenome    = 'phenome';
  36 my $sgn        = 'sgn';
  37 my $sgn_people = 'sgn_people';
  38 my $public     = 'public';
  39
  40 __PACKAGE__->selects_data("$phenome.locus.locus_id", "$phenome.locus.locus_name","$phenome.locus.locus_symbol",  "$phenome.allele.allele_name", "$phenome.allele.allele_symbol", "$phenome.allele.allele_synonym", "$phenome.allele.allele_phenotype", "$phenome.locus.obsolete", "$phenome.allele.obsolete", "$phenome.locus.sp_person_id", "$phenome.locus.description", "$phenome.locus.linkage_group", "$phenome.locus.lg_arm", "$sgn.common_name.common_name_id", "$sgn.common_name.common_name");
  41
  42
  43
  44 __PACKAGE__->join_root("$phenome.locus");
  45
  46 #join locus with allele table. Filter out obsolete alleles and the empty "default" alleles
  47 #(each locus should have one row in the allele table as a default space holder. This is important for making locus-stock associations, because these 2 are linked via the stockprop table, so that if we want to link a stock with a locus, without associating with a specific allele, the link will be made to the default allele_id)
  48 __PACKAGE__->uses_joinpath('allelepath',
  49                            [ "$phenome.allele", "$phenome.allele.locus_id=$phenome.locus.locus_id AND $phenome.allele.obsolete=false AND $phenome.allele.is_default=false" ],
  50                            );
  51
  52 __PACKAGE__->uses_joinpath('locusaliaspath', [ "$phenome.locus_alias", "$phenome.locus_alias.locus_id=$phenome.locus.locus_id"]);
  53
  54
  55 __PACKAGE__->uses_joinpath('locusmarkerpath', [ "$phenome.locus_marker", "$phenome.locus_marker.locus_id=$phenome.locus.locus_id"]);
  56 __PACKAGE__->uses_joinpath('locusunigenepath', [ "$phenome.locus_unigene", "$phenome.locus_unigene.locus_id=$phenome.locus.locus_id"]);
  57 __PACKAGE__->uses_joinpath('person_path',
  58                            ["$phenome.locus_owner", "$phenome.locus_owner.locus_id=$phenome.locus.locus_id"],
  59                            ["$sgn_people.sp_person", "$sgn_people.sp_person.sp_person_id=$phenome.locus_owner.sp_person_id"],
  60                            );
  61 __PACKAGE__->uses_joinpath('organism_path', [ "$sgn.common_name", "$sgn.common_name.common_name_id=$phenome.locus.common_name_id"]);
  62
  63
  64 __PACKAGE__->uses_joinpath('locusdbxrefpath',
  65                            [ "$phenome.locus_dbxref", "$phenome.locus_dbxref.locus_id=$phenome.locus.locus_id"],
  66                            [ "$public.dbxref", "$public.dbxref.dbxref_id=$phenome.locus_dbxref.dbxref_id"],
  67                            [ "$public.cvterm", "$public.dbxref.dbxref_id=$public.cvterm.dbxref_id"],
  68                            [ "$public.feature", "$public.dbxref.dbxref_id=$public.feature.dbxref_id"],
  69                            [ "public.cvtermsynonym", "$public.cvterm.cvterm_id=$public.cvtermsynonym.cvterm_id"],
  70                            [ "$public.db", "$public.dbxref.db_id=$public.db.db_id"],
  71                            );
  72
  73
  74 __PACKAGE__->has_parameter(name    => 'locus',
  75                            columns => "$phenome.locus.locus",
  76     );
  77
  78 __PACKAGE__->has_parameter(name    => 'locus_name',
  79                            columns => "$phenome.locus.locus_name",
  80                            );
  81
  82 __PACKAGE__->has_parameter(name    => 'locus_alias',
  83                            columns => "$phenome.locus_alias.alias",
  84                            group   =>1,
  85                            );
  86
  87 __PACKAGE__->has_parameter(name    => 'locus_alias_obsolete',
  88                            columns => "$phenome.locus_alias.obsolete",
  89                            group   =>1,
  90                            );
  91
  92 __PACKAGE__->has_parameter(name    => 'locus_id',
  93                            columns => "$phenome.locus.locus_id",
  94                            );
  95
  96
  97 __PACKAGE__->has_parameter(name    => 'locus_symbol',
  98                            columns => "$phenome.locus.locus_symbol",
  99                            );
 100
 101 __PACKAGE__->has_parameter(name    => 'allele_id',
 102                            columns => "$phenome.allele.allele_id",
 103                            );
 104 __PACKAGE__->has_parameter(name    => 'allele_name',
 105                            columns => "$phenome.allele.allele_name",
 106                            );
 107 __PACKAGE__->has_parameter(name    => 'allele_symbol',
 108                            columns => "$phenome.allele.allele_symbol",
 109                            );
 110
 111 __PACKAGE__->has_parameter(name    => 'allele_synonym',
 112                            columns => "$phenome.allele.allele_synonym",
 113                            sqlexpr => "array_to_string($phenome.allele.allele_synonym, ',')",
 114                            );
 115
 116 __PACKAGE__->has_parameter(name    => 'phenotype',
 117                            columns => "$phenome.allele.allele_phenotype",
 118                            );
 119
 120
 121 __PACKAGE__->has_parameter(name   =>'locus_obsolete',
 122                            columns=>"$phenome.locus.obsolete",
 123                            );
 124 __PACKAGE__->has_parameter(name   =>'allele_obsolete',
 125                            columns=>"$phenome.allele.obsolete",
 126                            );
 127
 128
 129 __PACKAGE__->has_parameter(name   =>'locus_description',
 130                            columns=>"$phenome.locus.description",
 131                            );
 132 __PACKAGE__->has_parameter(name   =>'locus_linkage_group',
 133                            columns=>"$phenome.locus.linkage_group",
 134                            );
 135 __PACKAGE__->has_parameter(name   =>'locus_lg_arm',
 136                            columns=>"$phenome.locus.lg_arm",
 137                            );
 138 __PACKAGE__->has_parameter(name   =>'common_name',
 139                            columns=>"$sgn.common_name.common_name",
 140                            );
 141 __PACKAGE__->has_parameter(name   =>'common_name_id',
 142                            columns=>"$sgn.common_name.common_name_id",
 143                            );
 144 __PACKAGE__->has_parameter(name   =>'editor',
 145                            columns=>["$sgn_people.sp_person.first_name",
 146                                      "$sgn_people.sp_person.last_name",
 147                                      "$sgn_people.sp_person.sp_person_id"],
 148                            sqlexpr=>"$sgn_people.sp_person.last_name || $sgn_people.sp_person.first_name
 149                                       || $sgn_people.sp_person.sp_person_id",
 150                            );
 151
 152 __PACKAGE__->has_parameter(name   =>'editor_id',
 153                            columns=>"$phenome.locus_owner.sp_person_id",
 154                            );
 155
 156 __PACKAGE__->has_parameter(name   =>'has_sequence',
 157                            columns=>["$phenome.locus_dbxref.locus_id"],
 158                            sqlexpr=>"count(distinct $phenome.locus_dbxref.locus_id)",
 159                            group  =>1,
 160                            aggregate=>1,
 161                            );
 162
 163
 164 __PACKAGE__->has_parameter(name   =>'has_marker',
 165                            columns=>["$phenome.locus_marker.locus_id"],
 166                            sqlexpr=>"count(distinct $phenome.locus_marker.locus_id)",
 167                            group  =>1,
 168                            aggregate=>1,
 169                            );
 170
 171 __PACKAGE__->has_parameter(name   =>'has_db_name',
 172                            columns=>"$public.db.name",
 173                            );
 174
 175 __PACKAGE__->has_parameter(name   =>'has_annotation',
 176                            columns=>["$phenome.locus_dbxref.dbxref_id"],
 177                            sqlexpr=>"count (distinct $phenome.locus_dbxref.locus_id)",
 178                            group  =>1,
 179                            aggregate=>1,
 180                            );
 181
 182 __PACKAGE__->has_parameter(name   =>'has_reference',
 183                            columns=>["$phenome.locus_dbxref.locus_id"],
 184                            sqlexpr=>"count (distinct $phenome.locus_dbxref.locus_id)",
 185                            group  =>1,
 186                            aggregate=>1,
 187                            );
 188
 189 __PACKAGE__->has_parameter(name   =>'cvterm_synonym',
 190                            columns=>"$public.cvtermsynonym.synonym",
 191                            );
 192
 193 __PACKAGE__->has_parameter(name   =>'ontology_term',
 194                            columns=>["$public.dbxref.accession",
 195                                      "$public.cvterm.name"],
 196                            sqlexpr=>"$public.cvterm.name ||  $public.dbxref.accession",
 197                            group  => 1,
 198                            );
 199
 200 __PACKAGE__->has_parameter(name   =>'genbank_accession',
 201                            columns=>["$public.feature.name",
 202                                      "$public.dbxref.accession"],
 203                            sqlexpr=>"$public.feature.name || $public.dbxref.accession",
 204                            group  => 1,
 205                            );
 206
 207
 208 __PACKAGE__->has_parameter(name   =>'default_allele',
 209                            columns=>"$phenome.allele.is_default",
 210                            group  =>1,
 211                            );
 212
 213 __PACKAGE__->has_complex_parameter( name => 'any_name',
 214                                     uses => [qw/locus locus_name locus_symbol locus_alias locus_description allele_symbol allele_name allele_synonym phenotype/],
 215                                     setter => sub {
 216                                       my ($self, @args) = @_;
 217                                       $self->locus(@args);
 218                                       $self->locus_name(@args);
 219                                       $self->locus_symbol(@args);
 220                                       $self->locus_alias(@args);
 221                                       $self->locus_description(@args);
 222                                       $self->allele_symbol(@args);
 223                                       $self->allele_name(@args);
 224                                       $self->allele_synonym(@args);
 225                                       $self->phenotype(@args);
 226
 227                                       $self->compound('&t OR &t OR &t OR &t OR &t OR &t OR &t OR &t OR&t' ,'locus' , 'locus_name', 'locus_symbol', 'locus_alias', 'locus_description', 'allele_symbol','allele_name', 'allele_synonym', 'phenotype');
 228                                     }
 229                                   );
 230
 231 ###### NOW WWW STUFF ###
 232
 233 sub request_to_params {
 234     my($self, %params) = @_;
 235
 236     #sanitize all the parameters
 237     foreach my $key (keys %params) {
 238         if( $params{$key} ) {
 239             $params{$key} =~ s/[;\'\",]//g;
 240             $params{$key} =~ s/^\s+//;
 241             $params{$key} =~ s/\s+$//;
 242         }
 243     }
 244
 245     $self->locus_obsolete("='f'");
 246
 247     if($params{any_name}) {
 248         my $any_name = $params{any_name};
 249         if ($any_name =~ m/(^solyc\d\dg\d{6})(\.*)/i ) { $any_name = substr($any_name, 0, 14); } #remove versions from solyc ids
 250         $self->conditional_like_from_scalars('any_name',
 251                                              @params{qw/any_name_matchtype/} , $any_name
 252                                              );
 253     }
 254
 255     if($params{phenotype}) {
 256         $self->phenotype('ILIKE ?',"%$params{phenotype}%");
 257         #$self->ind_phenotype('ILIKE ?',"%$params{phenotype}%");
 258         #$self->compound('&t OR &t', 'phenotype','ind_phenotype');
 259     }
 260
 261     if($params{common_name}) {
 262         $self->common_name('= ?', "$params{common_name}");
 263     }
 264
 265     #if ($params{editor} =~ m/^\d/) {
 266 #       $self->editor('= ?', "$params{editor}");
 267     if ($params{editor}) {
 268         $self->editor('ILIKE ?', "%$params{editor}%");
 269     }
 270
 271     if ($params{has_sequence}) {
 272         $self->has_sequence('>0');
 273         $self->has_db_name("= 'DB:GenBank_GI'");
 274         $self->terms_combine_op('AND');
 275     }
 276     if ($params{has_marker}) {
 277         $self->has_marker('!=0');
 278     }
 279     if ($params{has_annotation} && !$params{has_reference}) {
 280         $self->has_annotation('=1');
 281         $self->has_db_name("IN ('GO', 'PO', 'SP')");
 282         $self->terms_combine_op('AND');
 283     }
 284     if ($params{has_reference} && !$params{has_annotation}) {
 285         $self->has_reference('=1');
 286         $self->has_db_name("= 'PMID'");
 287         $self->terms_combine_op('AND');
 288     }
 289     if ($params{locus_linkage_group}) {
 290         $self->locus_linkage_group('= ?', "$params{locus_linkage_group}");
 291     }
 292
 293     if ($params{ontology_term}) {
 294         if ($params{ontology_term} =~m /(..)(:)(\d+)/i) {  #PO: | GO: | SP:
 295             $self->has_db_name('ILIKE ?', "$1");
 296             $self->ontology_term('ILIKE ?', "%$3%");
 297             $self->terms_combine_op('AND');
 298
 299         }else {
 300             $self->has_db_name("IN ('GO', 'PO', 'SP')");
 301             $self->cvterm_synonym('ILIKE ?', "%$params{ontology_term}%");
 302             $self->ontology_term('ILIKE ?', "%$params{ontology_term}%");
 303             $self->compound('&t AND (&t OR &t)','has_db_name','ontology_term', 'cvterm_synonym');
 304         }
 305     }
 306
 307     if ($params{genbank_accession}) {
 308         $self->genbank_accession('ILIKE ?', "%$params{genbank_accession}%");
 309     }
 310
 311     #page number
 312     if( defined($params{page}) ) {
 313         $self->page($params{page});
 314     }
 315 }
 316
 317 sub _to_scalars {
 318     my $self= shift;
 319     my $search= shift;
 320     my %params;
 321
 322     no warnings 'uninitialized';
 323
 324     #this part defines the mapping from get/post data to search params
 325     @params{qw/any_name_matchtype any_name/} = $self->conditional_like_to_scalars('any_name');
 326
 327
 328     ($params{phenotype}) = $self->param_bindvalues('phenotype');
 329     $params{phenotype} =~ s/%//g;
 330
 331     ($params{allele_obsolete}) = $self->param_bindvalues('allele_obsolete');
 332     $params{allele_obsolete} =~ s/%//g;
 333
 334     ($params{common_name}) = $self->param_bindvalues('common_name');
 335     ($params{common_name_id}) = $self->param_bindvalues('common_name_id');
 336
 337     ($params{editor}) = $self->param_bindvalues('editor');
 338     $params{editor} =~ s/%//g;
 339
 340
 341     $params{has_sequence} = $self->pattern_match_parameter('has_sequence', qr/>\s*0/);
 342     $params{has_marker} = $self->pattern_match_parameter('has_marker', qr/!=\s*0/);
 343
 344     $params{has_annotation} = $self->pattern_match_parameter('has_annotation', qr/!=\=1/);
 345     $params{has_annotation} = $self->pattern_match_parameter('has_db_name', qr/PO|GO|SP/);
 346
 347     $params{has_reference} = $self->pattern_match_parameter('has_reference', qr/=1/);
 348     $params{has_reference} = $self->pattern_match_parameter('has_db_name', qr/PMID/);
 349
 350     ($params{locus_linkage_group}) = $self->param_bindvalues('locus_linkage_group');
 351
 352     ($params{ontology_term}) = $self->param_bindvalues('ontology_term');
 353     $params{ontology_term} =~ s/%//g;
 354     ($params{has_db_name}) = $self->param_bindvalues('has_db_name');
 355
 356     if ( $params{has_db_name} ) {
 357         $params{ontology_term} = $params{has_db_name} . ":" . $params{ontology_term};
 358     }
 359
 360     ($params{genbank_accession}) = $self->param_bindvalues('genbank_accession');
 361     $params{genbank_accession} =~ s/%//g;
 362
 363
 364     return %params;
 365 }
 366
 367 sub to_html {
 368     my $self = shift;
 369     my $search = 'advanced';
 370     my %scalars = $self->_to_scalars($search);
 371
 372     #make %pname, a tied hash that uniqifies names the make_pname
 373     # function is in CXGN::Page::WebForm, which is a parent of
 374     # CXGN::Search::DBI::Simple::WWWQuery
 375     $self->make_pname;
 376     our %pname;
 377
 378     my $any_name_select = conditional_like_input_html($pname{any_name}, $scalars{any_name_matchtype}, $scalars{any_name}, '30');
 379
 380     my $dbh=_cached_dbh();
 381     my ($organism_names_ref, $organism_ids_ref) = CXGN::Tools::Organism::get_existing_organisms($dbh);
 382     #add an empty entry to the front of the list
 383     unshift @$organism_names_ref, '';
 384
 385     my $organism = simple_selectbox_html( choices  => $organism_names_ref,
 386                                           name     => $pname{common_name},
 387                                           selected => $scalars{common_name},
 388                                           );
 389
 390     my ($lg_names_ref) = CXGN::Phenome::Locus::LinkageGroup::get_all_lgs($dbh);
 391     my @lg_options = ();
 392
 393     for(my $i = 0; $i < scalar(@$lg_names_ref); $i++) {
 394         push @lg_options, [$lg_names_ref->[$i], $lg_names_ref->[$i]];
 395     }
 396
 397     my $linkage_group_select = simple_selectbox_html( choices  => \@lg_options,
 398                                                       name     => $pname{locus_linkage_group},
 399                                                       selected => $scalars{locus_linkage_group},
 400                                                       );
 401
 402     my $has_sequence= $self->uniqify_name('has_sequence');
 403     my $has_marker = $self->uniqify_name('has_marker');
 404     my $has_annotation= $self->uniqify_name('has_annotation');
 405     my $has_reference= $self->uniqify_name('has_reference');
 406     my $ontology_term = $self->uniqify_name('ontology_term');
 407     my $genbank_accession = $self->uniqify_name('genbank_accession');
 408
 409     #check boxes
 410     @scalars{qw/has_sequence has_marker has_annotation has_reference/} =
 411         map {$_ ? 'checked="checked" ' : undef} @scalars{qw/has_sequence has_marker has_annotation has_reference/};
 412
 413     my $show_advanced_search =
 414         grep {defined($_)} @scalars{qw/ common_name phenotype editor has_sequence
 415                                         locus_linkage_group has_marker
 416                                         has_annotation has_reference
 417                                         ontology_term genbank_accession
 418                                         /};
 419     no warnings 'uninitialized';
 420
 421     my $advanced_search=
 422         html_optional_show('advanced_search',
 423                            'Advanced search options',
 424                            qq|<div class="minorbox">\n|
 425                            .info_table_html(
 426                                             'Organism'   => $organism,
 427                                             'Chromosome / Linkage&nbsp;Group' => $linkage_group_select,
 428                                             'Locus editor' =>qq|<input name="$pname{editor}" value="$scalars{editor}" size="20"/>|,
 429                                             'Show only genes with' => <<EOH,
 430                                             <input type="checkbox" name="$has_sequence" $scalars{has_sequence} />sequence <br />
 431                                             <input type="checkbox" name="$has_marker" $scalars{has_marker} />markers<br />
 432                                             <input type="checkbox" name="$has_annotation" $scalars{has_annotation} />GO/PO annotation<br />
 433 EOH
 434                                             'Phenotype'  => qq|<input name="$pname{phenotype}" value="$scalars{phenotype}" size="30" /><a href="direct_search.pl?search=phenotypes"> [Advanced SGN phenotype search]</a>|,
 435                                             'Ontology term' => qq|<input name="$ontology_term" value = "$scalars{ontology_term}" />
 436                                             <br /><span class="ghosted">(Term name or ID: e.g. 'carotenoid' or 'PO:0007010')</span>|,
 437                                             'Genbank ID' =>qq|<input name="$genbank_accession" value="$scalars{genbank_accession}"
 438                                             <br /><span class="ghosted">(Accession or GI: e.g. 'EF091820' or '118185006')</span>|,
 439                                             #'Associated publication' => "pubmedID insert text area/check box",
 440                                             __border   =>0,
 441                                             __multicol =>2,
 442                                             __tableattrs => 'width="100%"',
 443                                             ) .qq|</div>|,
 444                            $show_advanced_search);
 445
 446     my $html_ret = <<EOHTML;
 447
 448     <table><tr>
 449         <td colspan="2"><b>Search for any locus or allele</b>  (<a href="../help/gene_search_help.pl">gene search help page</a>)</td></tr>
 450         <tr><td>$any_name_select</td>
 451         <td><a href="../phenome/locus_display.pl?action=new">[Submit new locus]</a></td>
 452         </tr></table>
 453         <br />
 454         $advanced_search
 455         <div align="center"><input type="submit" value="Search"/></div>
 456 EOHTML
 457 }
 458
 459 sub quick_search {
 460     my ($self,$term) = @_;
 461     $self->any_name('ILIKE ?', "%$term%");
 462     $self->locus_obsolete('=?', "f");
 463     #$self->allele_obsolete('=?', "f");
 464     return $self;
 465 }
 466
 467 ###
 468 1;#do not remove
 469 ###