mason/stock/index.mas

   1 <%doc>
   2
   3 =head1 NAME
   4
   5 /stock/index.mas - a page for displaying stock details (e.g. accession, population, etc.)
   6
   7 =head1 DESCRIPTION
   8
   9 parameters:
  10
  11 =over 1
  12
  13 =item $stockref
  14
  15 a hashref with all the parameters needed for printing the stock page!
  16
  17  $stockref->{stock_id}
  18  $stockref->{stock}
  19  $stockref->{schema}
  20  $stockref->{uniquename}
  21  $stockref->{curator}  (boolean)
  22  $stockref->{submitter} (boolean)
  23  $stockref->{is_owner} (boolean)
  24  $stockref->{props} (hash of arrayrefs of stockprops. Keys = prop name, value = prop value)
  25  $stockref->{has_pedigree} (boolean)
  26  $stockref->{has_descendants} (boolean)
  27  locus_add_uri
  28  locus_autocomplete_uri => '/ajax/locus/autocomplete/'
  29  cvterm_add_uri
  30  cvterm_autocomplete_uri => '/ajax/cvterm/autocomplete/'
  31  barcode_tempdir
  32  barcode_tempuri
  33  organism_autocomplete_uri => '/ajax/organism/autocomplete/'
  34
  35 =back
  36
  37 =head1 AUTHOR
  38
  39 Naama Menda <nm249@cornell.edu>
  40
  41 =cut
  42
  43 </%doc>
  44
  45 <%args>
  46 $stock_row
  47 $stockref => undef
  48 $locus_add_uri => ''
  49 $locus_autocomplete_uri => undef
  50 $cvterm_add_uri => ''
  51 $cvterm_autocomplete_uri => undef
  52 $barcode_tempdir => undef
  53 $barcode_tempuri => undef
  54 $identifier_prefix => 'SGN'
  55 $organism_autocomplete_uri => '/ajax/organism/autocomplete/'
  56
  57 </%args>
  58
  59
  60 <%perl>
  61
  62 use Bio::Chado::Schema;
  63 use CXGN::Chado::Stock;
  64 use CXGN::Page::FormattingHelpers qw / html_optional_show info_table_html /;
  65 use CXGN::People::Person;
  66 use CXGN::Chado::Publication;
  67 use CXGN::Cview::Map::SGN::Genotype;
  68 use CXGN::Cview::MapOverviews;
  69
  70 my $stock = $stockref->{stock};
  71 my $stock_id = $stockref->{stock_id};
  72 my $action = $stockref->{action} || 'view';
  73 my $person_id = $stockref->{person_id};
  74 my $curator = $stockref->{curator};
  75 my $submitter = $stockref->{submitter};
  76 my $sequencer = $stockref->{sequencer};
  77 my $pubs = $stockref->{pubs};
  78 my $has_pedigree = $stockref->{has_pedigree};
  79 my $has_descendants = $stockref->{has_descendants};
  80 my $trait_ontology_db_name = $stockref->{trait_ontology_db_name};
  81 my $editable_stock_props_string = $stockref->{editable_stock_props};
  82 my $schema = $stockref->{schema};
  83 my $dbh = $stockref->{dbh};
  84
  85 my @editable_stock_props = split "," , $editable_stock_props_string;
  86
  87 my $stockprop_cv = $schema->resultset("Cv::Cv")->search( {
  88  'me.name' => 'stock_property'} );
  89
  90
  91 my ($type_name, $uniquename);
  92 my $type = $stock_row ? $stock_row->type : undef;
  93 $type_name  = $type->name() if $type;
  94 $uniquename = $stock->get_uniquename if $type;
  95 #################
  96 my $is_owner = $stockref->{is_owner};
  97
  98 my $this_page = "/stock/$stock_id/view";
  99
 100 my $add_image_link = qq|<a href="/image/add?type_id=$stock_id&action=new&type=stock&refering_page=$this_page">[Add new image]</a>|;
 101 my $image_ids =  $stockref->{image_ids} || [] ;
 102 my $stockprops = $stockref->{props};
 103
 104 ###this is replaced by $editable_stock_props. Needs to be provided in the conf file
 105 my $metadata = ['variety', 'donor', 'donor institute', 'country', 'state' , 'adaptation' , 'notes', 'GSOR', 'NPGS', 'Gpno', 'IRGSP', 'NSFTV', 'CIor', 'PI', 'subpopulation'];
 106 ####
 107
 108
 109 #my $pedigree= ['pedigree', 'male parent', 'female parent'];
 110 # get pedigree of stock
 111 #my $stock_pedigree = $stockref->{stock_pedigree};
 112 #my $stock_descendants = $stockref->{stock_descendants};
 113
 114
 115 my $experiment = ['year', 'location', 'replicate']; # these values should be in nd_experimentprop ?
 116
 117 my $resources = [ 'stock_synonym', 'solcap number'];
 118
 119 my $allele_div = "stock_alleles";
 120 my $new_locus_link = !$person_id ? qq|<a href="/solpeople/login.pl">[log-in to associate new locus]</a> | : '' ;
 121
 122 #owner
 123 my $owners = $stockref->{owners};
 124 my $editor_link;
 125 foreach my $o_id (@$owners) {
 126   my $person = CXGN::People::Person->new($dbh, $o_id);
 127   my $first_name = $person->get_first_name;
 128   my $last_name = $person->get_last_name;
 129   $editor_link .= qq|<a href="/solpeople/personal-info.pl?sp_person_id=$o_id">$first_name $last_name</a> |;
 130 }
 131
 132 #phenotypes measured directly on this stock
 133 my $direct_phenotypes = $stockref->{direct_phenotypes} || undef;
 134
 135 # get all phenotypes of subjects
 136 my $members_phenotypes = $stockref->{members_phenotypes};
 137 my $p_download_link = qq|<a href = "/stock/$stock_id/phenotypes">[Download phenotypes]</a>| if ( (keys %$direct_phenotypes) || ( keys %$members_phenotypes) );
 138 my $direct_genotypes = $stockref->{direct_genotypes};
 139 my $g_download_link = qq|<a href =  "/stock/$stock_id/genotypes">Download genotypes</a>| if (keys %$direct_genotypes) ;
 140 ############################
 141 my $map_html = $stockref->{map_html};
 142 my $map;
 143 if ($stock_id) {
 144   $map = CXGN::Cview::Map::SGN::Genotype->new($dbh, $stock_id);
 145   if ($map->get_chromosome_count > 1 ) {
 146     my $overview = CXGN::Cview::MapOverviews::Generic->new($map,
 147                                                            {
 148                                                             dbh=> $dbh,
 149                                                             basepath => $stockref->{cview_basepath},
 150                                                             tempfiles_subdir => $stockref->{cview_tmp_dir } });
 151     if ($overview) {
 152       $overview->render_map();
 153       $map_html .= $overview->get_image_html();
 154     }
 155   }
 156 }
 157 #########################################
 158 my $has_qtl_data = $stockref->{has_qtl_data};
 159
 160
 161 my $new_pub_link = $curator || $submitter || $sequencer  ?   qq|<a href="/chado/add_publication.pl?type=stock&amp;type_id=$stock_id&amp;refering_page=$this_page&amp;action=new"> [Associate publication] </a>| : qq|<span class=\"ghosted\">[Associate publication]</span>| ;
 162
 163 my $pub_count = scalar( keys %$pubs );
 164
 165 ## EUSOL, tgrc (stock_dbxref)
 166 my $dbxrefs = $stockref->{dbxrefs};
 167 my %source_dbs;
 168 foreach my $db_name ( keys %$dbxrefs ) {
 169   foreach my $dbxref ( @{ $dbxrefs->{$db_name} } ) {
 170     my $url = $dbxref->db->urlprefix . $dbxref->db->url;
 171     $url .= $dbxref->accession if $url =~ m/\?$|\=$/ ;
 172     $source_dbs{$url} = $db_name . ": " . $dbxref->accession if $url;
 173   }
 174 }
 175
 176 my $ontology_subtitle = $curator || $submitter || $sequencer  ?
 177   qq|<a href="javascript:Tools.toggleContent('associate_cvterm_form', 'stock_ontology')">[Add ontology annotations]</a> | :
 178   qq |<span class = "ghosted"> [Add ontology annotations]</span> |;
 179
 180 my $add_phenotype_link =  $curator || $submitter || $sequencer  ? qq| <a href="javascript:Tools.toggleContent('add_phenotype_form', 'stock_phenotype')" >[Add phenotype]</a> | :   qq |<span class = "ghosted"> [Add phenotype]</span> |;
 181
 182 my $edit_privs = $curator || $submitter || $sequencer;
 183
 184 my $project_name = lc($c->config->{project_name});
 185 my $test_url = "/jbrowse_$project_name/current/data/json/accessions/" . $stock_id . "/trackList.json";
 186 my $jbrowse_url = "/jbrowse/?data=data%2Fjson%2Faccessions%2F" . $stock_id . "&tracks=DNA%2CGene%20exons%2C" . $uniquename . "_2015_V6_imputed&highlight=";
 187
 188 </%perl>
 189 <& /util/import_javascript.mas, classes => ["jquery", "jqueryui", "thickbox", "CXGN.Page.FormattingHelpers", "jquery.cookie", "CXGN.Stock"] &>
 190
 191
 192 <script language="javascript">
 193 function jqueryStuff() {
 194    jQuery(function() {
 195      jQuery("#species_name").autocomplete({
 196         source: '/organism/autocomplete'
 197      });
 198   });
 199 }
 200 </script>
 201 <& /page/page_title.mas, title=> join( ': ', grep $_, ucfirst($type_name), $uniquename ) || 'Create a new stock' &>
 202
 203
 204 <&| /page/info_section.mas, title=>"Stock details" , subtitle => "<a href=/phenome/qtl_form.pl>New QTL population</a> | <a href=/search/stocks/>Back to stock search</a>"  &>
 205
 206 <div class="row">
 207   <div class="col-sm-6">
 208
 209   <& /page/form.mas,
 210   object_type=>'stock',
 211   object_id=>"$stock_id",
 212   form_name=> 'stock_form',
 213   server_side_script => '/phenome/stock/stock_ajax_form.pl',
 214   form_div_name=>'stock_details',
 215   js_object_name=> 'stockForm',
 216   page_url => "/stock/$stock_id/view/" ,
 217   alternate_new_button => '<a href ="/stock/0/new">[New]</a>'
 218   &>
 219
 220   </div>
 221   <div class="col-sm-6">
 222 <& /util/barcode.mas, identifier => "$identifier_prefix"."$stock_id", text=> "$identifier_prefix stock $stock_id ($uniquename)", format=>"code128"  &><br /><br />
 223 % #<& /util/barcode.mas, identifier => "http://solgenomics.net/stock/$stock_id/view", text=>"SGN stock $stock_id ($uniquename)", format=>"qrcode" &>
 224
 225   </div>
 226 </div>
 227
 228 <div><b>Stock editors: </b> <% $editor_link %></div>
 229 <br />
 230 % foreach my $db_url (keys %source_dbs) {
 231 <div><a href=<% $db_url %>><% $source_dbs{$db_url} %></a> </div>
 232 %}
 233 <br />
 234 % my $div_name = join("_", @$resources);
 235 % my $subtitle = $edit_privs ? "[<a id=\"stock_add_synonym\" href=\"javascript:synonyms_addPropDialog()\">Add...</a>]" : "[Add]";
 236    <&| /page/info_section.mas, title => "Synonyms" , is_subsection => 1 , subtitle=>$subtitle &>
 237       <& /stock/stockprops.mas,
 238        stock_id    => $stock_id,
 239         props      => $stockprops ,
 240         div_name   =>'synonyms',
 241         subset     =>$resources,
 242         editable   => [ 'stock_synonym' ],
 243         edit_privs => $edit_privs   &>
 244 </&>
 245 %  $div_name = join("_", @editable_stock_props);
 246 % my $props_subtitle = $edit_privs ? "[<a id=\"stock_add_props\" href=\"javascript:stockprops_addPropDialog()\">Add...</a>]" : "[Add]";
 247
 248     <&| /page/info_section.mas, title => "Additional information" , collapsible=> 1, is_subsection => 1, subtitle=>$props_subtitle &>
 249       <& /stock/stockprops.mas,
 250          stock_id  =>$stock_id,
 251         props      => $stockprops,
 252         div_name   => 'stockprops',
 253         edit_privs => $edit_privs,
 254         subset     => \@editable_stock_props,
 255         editable   => \@editable_stock_props  &>
 256 </&>
 257
 258
 259 </&>
 260
 261
 262 <&| /page/info_section.mas, title => "Associated loci (" . $stockref->{allele_count} . ")" , subtitle => $new_locus_link, collapsible=> 1 , collapsed => 1 &>
 263
 264 <& /phenome/associate_locus.mas, object_id => $stock_id , object_name => "stock", locus_add_uri=> $locus_add_uri,   allele_div => $allele_div , show_form => $is_owner &>
 265
 266 </&>
 267
 268
 269 <&| /page/info_section.mas, title => "Experimental data" , collapsible=> 1, is_subsection => 0 &>
 270       <& /stock/stockprops.mas, stock_id=>$stock_id, props=> $stockprops, subset=> $experiment  &>
 271 </&>
 272
 273 % if($is_owner) {
 274 <&| /page/info_section.mas, title=>"Stock history", collapsible=>1, collapsed=>1 &>
 275
 276 </&>
 277
 278
 279 % }
 280
 281 <%perl>
 282  my $collapsible = 0;
 283  if ($has_pedigree==1) {
 284   $collapsible = 1;
 285  }
 286  my $add_parent_link = "Add parent";
 287  if ($person_id && ($submitter || $curator || $sequencer)) { $add_parent_link = qq | <a id="add_parent_link" >Add parent</a> |; }
 288
 289 my $remove_parent_link = "Remove parent";
 290 if ($person_id && ($submitter || $curator || $sequencer)) { $remove_parent_link = qq | <a id="remove_parent_link">Remove parent</a> |; }
 291
 292 </%perl>
 293
 294 <div id="remove_parent_dialog">
 295 Remove a parent (this will only remove the link to the parent, not the parent accession itself).<br /><br />
 296   <div id="remove_parent_list">[loading parent list...]</div>
 297 </div>
 298
 299
 300 <&| /page/info_section.mas, title=>"Pedigree" , collapsible=> $collapsible, collapsed=>0, subtitle=>"[$add_parent_link] [$remove_parent_link]" &>
 301   <& /pedigree/stock_pedigree.mas, stock_id => $stock_id, has_pedigree => $has_pedigree &>
 302 </&>
 303
 304 % if ($has_descendants==1) {
 305
 306 <&| /page/info_section.mas, title=>"Descendants" , collapsible=>1, collapsed=>0 &>
 307   <& /pedigree/stock_descendants.mas, stock_id => $stock_id &>
 308 </&>
 309
 310 % } else {
 311
 312 <&| /page/info_section.mas, title=>"Descendants" , collapsible=>1, collapsed=>1 &>
 313 </&>
 314
 315 % }
 316
 317 <& /pedigree/stock_pedigree_string.mas, stock_id => $stock_id &>
 318
 319
 320 % if ($type) {
 321 <&| /page/info_section.mas, title=>"Related stocks" , collapsible=>1, collapsed=>0 &>
 322   <& /stock/related_stocks.mas, stock => $stock_row &>
 323
 324 </&>
 325
 326 % }
 327
 328
 329 <&| /page/info_section.mas, title=>"Images (" .  scalar(@$image_ids)  . ")", subtitle => "$add_image_link", collapsible=>1, collapsed=>1 &>
 330   <& /image/print_images.mas , images=>$image_ids , dbh=>$dbh &>
 331
 332 </&>
 333
 334
 335 <&| /page/info_section.mas, title=>"Literature annotation ($pub_count)" , subtitle=>$new_pub_link, id=>"publications" , collapsible=>1, collapsed=>1 &>
 336
 337 % my $pub_count = 0;
 338 % foreach my $full_accession ( keys %$pubs  ) {
 339 % my $pub = CXGN::Chado::Publication->new($dbh, $pubs->{$full_accession}->pub_id );
 340 % my ($pub_db_name, $accession) = split ':' , $full_accession;
 341 <& /chado/publication.mas, pub=>$pub, count=>$pub_count++, db=>$pub_db_name, accession=>$accession &>
 342   <br >
 343 % }
 344
 345 </&>
 346
 347 <&| /page/info_section.mas,
 348   id   => 'stock_ontology',
 349   title=>"Ontology annotation (" . $stockref->{ontology_count} . ")",
 350   collapsible=>1,
 351   collapsed=>1,
 352   subtitle=>$ontology_subtitle &>
 353   <& /ontology/associate_ontology.mas,
 354   trait_db_name => $trait_ontology_db_name,
 355   object_id     => $stock_id ,
 356   object_name   => "stock",
 357   cvterm_add_uri=> $cvterm_add_uri,
 358   ontology_url  => "/stock/$stock_id/ontologies/",
 359   reference_uri => "/stock/$stock_id/references/",
 360   evidence_with_uri => "/stock/$stock_id/evidences/",
 361   show_form     => $is_owner  &>
 362 </&>
 363
 364 <&| /page/info_section.mas, title=>"Phenotype data " ,  subtitle=>$p_download_link ,  collapsible => 1, collapsed => 1 &>
 365 % foreach my $project (keys %$direct_phenotypes) {
 366 %   my $rs = $direct_phenotypes->{$project} ;
 367
 368 <&| /page/info_section.mas,
 369     id       => "stock_phenotype",
 370     title    =>"Experiment: $project",
 371     subtitle => $add_phenotype_link,
 372     is_subsection => 1,
 373     collapsible => 1
 374 &>
 375     <& /stock/add_phenotype.mas,
 376       stock_id => $stock_id ,
 377       trait_ontology_db_name => $trait_ontology_db_name,
 378       project=>$project
 379     &>
 380   <& /phenotypes/phenotype_data.mas ,
 381       phenotypes=> $rs
 382     &>
 383   </&>
 384 % }
 385
 386 % foreach my $key (keys %$members_phenotypes) {
 387 % my $m_rs = $members_phenotypes->{$key};
 388 <&| /page/info_section.mas,
 389      title         => "Member phenotypes",
 390      subtitle      => $key,
 391      is_subsection => 1,
 392      collapsible   => 1,
 393  &>
 394     <& /phenotypes/phenotype_data.mas,
 395          phenotypes => $m_rs,
 396          object_id  => $stock_id,
 397          has_qtl    => $has_qtl_data,
 398      &>
 399   </&>
 400 % }
 401 </&>
 402
 403 <div id="stock_trials_info_popup">
 404   <table id="stock_trials_info_table" >
 405     <thead>
 406     <tr><th>Trait</th><th>Average</th><th>Std dev</th></tr>
 407     </thead>
 408   </table>
 409 </div>
 410
 411 <link rel="stylesheet" type="text/css" href="/documents/inc/datatables/jquery.dataTables.css">
 412
 413
 414 <&| /page/info_section.mas, title => "Trials" &>
 415
 416   <& /stock/trials.mas, stock_id => $stock_id &>
 417
 418 </&>
 419
 420 <&| /page/info_section.mas, title => "Traits assayed" &>
 421
 422   <& /stock/traits.mas, stock_id => $stock_id &>
 423
 424 </&>
 425
 426 %#<&| /page/info_section.mas, title => "Phenotypic data" &>
 427
 428 %#  <& /stock/phenotypes.mas, stock_id => $stock_id &>
 429
 430 %#</&>
 431
 432 <&| /page/info_section.mas, title=>"Genotype data ", subtitle=> $g_download_link, collapsible => 1 , collapsed => 1 &>
 433 % print $map_html;
 434 % foreach my $project (keys %$direct_genotypes) {
 435 %  my $genotypes = $direct_genotypes->{$project} ;
 436 <&| /page/info_section.mas, title=>"Experiment: $project", is_subsection => 1, collapsible => 1 &>
 437 % foreach my $genotype (@$genotypes) {
 438 %  print $genotype->description . "\n";
 439 % }
 440   </&>
 441 % }
 442 </&>
 443
 444
 445 <&| /page/info_section.mas, title=>"Accession JBrowse", collapsible => 1 , collapsed => 0 &>
 446 <p id="jbrowse_check">[loading...]</p>
 447 </&>
 448
 449
 450 <& /page/comments.mas, object_type=>'stock', object_id=>$stock_id, referer=>$this_page &>
 451
 452
 453 <script>
 454   jQuery(document).ready(function() {
 455     stock_detail_page_init_dialogs();
 456     prepareJbrowse();
 457
 458     jQuery('#remove_parent_link').click( function() {
 459       jQuery('#remove_parent_dialog').dialog("open");
 460       get_remove_parents_list(<% $stock_id %>);
 461     });
 462
 463     function prepareJbrowse () { //ajax function to test for existence of given jbrowse trial url
 464     jQuery.ajax({
 465     type: 'GET',
 466     url: "<% $test_url %>",
 467     statusCode: {
 468         200: function () {  // if page is found, create and display link
 469                 jQuery('#jbrowse_check').replaceWith('<a id="jbrowse_link" href="<% $jbrowse_url %>">View vcf tracks for <% $uniquename %> in JBrowse</a>');
 470         },
 471         404: function () { // if page not found, display message that jbrowse instance wasn't found
 472                 jQuery('#jbrowse_check').html(" <i>No Jbrowse instance found for this accession</i>.");
 473                 }
 474         }
 475   });
 476   }
 477
 478 });
 479 </script>