package SGN::View::Mason::Commands; use strict; use vars qw($m $c); HTML::Mason::Component::FileBased->new( 'code' => sub { use utf8; local $SGN::View::Mason::Commands::m = $HTML::Mason::Commands::m; HTML::Mason::Exception::Params->throw ( error => "Odd number of parameters passed to component expecting name/value pairs" ) if @_ % 2; my ( $stock_row, $stockref, $locus_add_uri, $locus_autocomplete_uri, $cvterm_add_uri, $cvterm_autocomplete_uri, $barcode_tempdir, $barcode_tempuri, $identifier_prefix, $organism_autocomplete_uri, $image, $image_url ); { my %pos; for ( my $x = 0; $x < @_; $x += 2 ) { $pos{ $_[$x] } = $x + 1; } foreach my $arg ( qw( stock_row ) ) { HTML::Mason::Exception::Params->throw ( error => "no value sent for required parameter '$arg'" ) unless exists $pos{$arg}; } #line 46 "/home/production/cxgn/sgn/mason/stock/index.mas" $stock_row = $_[ $pos{'stock_row'} ]; #line 47 "/home/production/cxgn/sgn/mason/stock/index.mas" $stockref = exists $pos{'stockref'} ? $_[ $pos{'stockref'} ] : undef; #line 48 "/home/production/cxgn/sgn/mason/stock/index.mas" $locus_add_uri = exists $pos{'locus_add_uri'} ? $_[ $pos{'locus_add_uri'} ] : ''; #line 49 "/home/production/cxgn/sgn/mason/stock/index.mas" $locus_autocomplete_uri = exists $pos{'locus_autocomplete_uri'} ? $_[ $pos{'locus_autocomplete_uri'} ] : undef; #line 50 "/home/production/cxgn/sgn/mason/stock/index.mas" $cvterm_add_uri = exists $pos{'cvterm_add_uri'} ? $_[ $pos{'cvterm_add_uri'} ] : ''; #line 51 "/home/production/cxgn/sgn/mason/stock/index.mas" $cvterm_autocomplete_uri = exists $pos{'cvterm_autocomplete_uri'} ? $_[ $pos{'cvterm_autocomplete_uri'} ] : undef; #line 52 "/home/production/cxgn/sgn/mason/stock/index.mas" $barcode_tempdir = exists $pos{'barcode_tempdir'} ? $_[ $pos{'barcode_tempdir'} ] : undef; #line 53 "/home/production/cxgn/sgn/mason/stock/index.mas" $barcode_tempuri = exists $pos{'barcode_tempuri'} ? $_[ $pos{'barcode_tempuri'} ] : undef; #line 54 "/home/production/cxgn/sgn/mason/stock/index.mas" $identifier_prefix = exists $pos{'identifier_prefix'} ? $_[ $pos{'identifier_prefix'} ] : 'SGN'; #line 55 "/home/production/cxgn/sgn/mason/stock/index.mas" $organism_autocomplete_uri = exists $pos{'organism_autocomplete_uri'} ? $_[ $pos{'organism_autocomplete_uri'} ] : '/ajax/organism/autocomplete/'; #line 56 "/home/production/cxgn/sgn/mason/stock/index.mas" $image = exists $pos{'image'} ? $_[ $pos{'image'} ] : undef; #line 57 "/home/production/cxgn/sgn/mason/stock/index.mas" $image_url = exists $pos{'image_url'} ? $_[ $pos{'image_url'} ] : undef; } $m->debug_hook( $m->current_comp->path ) if ( HTML::Mason::Compiler::IN_PERL_DB() ); #line 44 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 59 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 61 "/home/production/cxgn/sgn/mason/stock/index.mas" use Bio::Chado::Schema; use CXGN::Chado::Stock; use CXGN::Page::FormattingHelpers qw / html_optional_show info_table_html /; use CXGN::People::Person; use CXGN::Chado::Publication; use CXGN::Cview::Map::SGN::Genotype; use CXGN::Cview::MapOverviews; use SGN::Image; my $trial_stock_type => undef; my $stock = $stockref->{stock}; my $stock_id = $stockref->{stock_id}; my $action = $stockref->{action} || 'view'; my $person_id = $stockref->{person_id}; my $curator = $stockref->{curator}; my $submitter = $stockref->{submitter}; my $sequencer = $stockref->{sequencer}; my $pubs = $stockref->{pubs}; my $has_pedigree = $stockref->{has_pedigree}; my $has_descendants = $stockref->{has_descendants}; my $trait_ontology_db_name = $stockref->{trait_ontology_db_name}; my $editable_stock_props_string = $stockref->{editable_stock_props}; my $schema = $stockref->{schema}; my $dbh = $stockref->{dbh}; my $is_obsolete = $stockref->{is_obsolete}; my $is_a_transgenic_line = $stockref->{is_a_transgenic_line}; my $is_in_trial = $stockref->{is_in_trial}; my @editable_stock_props = split "," , $editable_stock_props_string; my ($type_name, $uniquename); my $type = $stock_row ? $stock_row->type : undef; $type_name = $type->name() if $type; $uniquename = $stock->get_uniquename if $type; my @editable_vector_props; if($type_name eq 'vector_construct'){ my $editable_vector_props_string = $stockref->{editable_vector_props}; @editable_vector_props = split "," , $editable_vector_props_string; } ################# my $is_owner = $stockref->{is_owner}; my $this_page = "/stock/$stock_id/view"; my $image_ids = $stockref->{image_ids} || [] ; my $related_image_ids = $stockref->{related_image_ids} || [] ; my $stockprops = $stockref->{props}; my @valid_image_ids; foreach my $image (@$image_ids) { my $image_id = $image->[0]; my $image_obj = SGN::Image->new($schema->storage->dbh, $image_id, $c); if ($image_obj->get_md5sum()) { push(@valid_image_ids, $image) } } $image_ids = \@valid_image_ids; #my $pedigree= ['pedigree', 'male parent', 'female parent']; # get pedigree of stock #my $stock_pedigree = $stockref->{stock_pedigree}; #my $stock_descendants = $stockref->{stock_descendants}; my $allele_div = "stock_alleles"; my $new_locus_link = !$person_id ? qq|[log-in to associate new locus] | : '' ; #owner my $owners = $stockref->{editor_info}; my $owner_ids = $stockref->{owners}; my $owners_html = ''; my %unique_owners; foreach my $o_id (@$owner_ids) { $unique_owners{$o_id}++; } my @owner_ids = keys %unique_owners; foreach my $o_id (@owner_ids){ my $person = CXGN::People::Person->new($dbh, $o_id); my $first_name = $person->get_first_name; my $last_name = $person->get_last_name; $owners_html .= qq|$first_name $last_name |; } my $editor_link_table; if ($is_obsolete) { $editor_link_table = ""; foreach my $o_id (@$owners) { my $person = CXGN::People::Person->new($dbh, $o_id->[0]); my $first_name = $person->get_first_name; my $last_name = $person->get_last_name; $editor_link_table .= qq||; } } else { $editor_link_table = "
EditorTimestampModification NoteObsolete Note
$first_name $last_name$o_id->[1]$o_id->[2]$o_id->[3]
"; foreach my $o_id (@$owners) { my $person = CXGN::People::Person->new($dbh, $o_id->[0]); my $first_name = $person->get_first_name; my $last_name = $person->get_last_name; $editor_link_table .= qq||; } } $editor_link_table .= "
EditorTimestampModification Note
$first_name $last_name$o_id->[1]$o_id->[2]
"; $editor_link_table = "
".$owners_html."

".$editor_link_table; #phenotypes measured directly on this stock my $direct_phenotypes = $stockref->{direct_phenotypes} || undef; # get all phenotypes of subjects my $members_phenotypes = $stockref->{members_phenotypes}; my $p_download_link = 'Download All Phenotypes'; ############################ my $map_html = $stockref->{map_html}; my $map; if ($stock_id) { $map = CXGN::Cview::Map::SGN::Genotype->new($dbh, $stock_id); if ($map->get_chromosome_count > 1 ) { my $overview = CXGN::Cview::MapOverviews::Generic->new($map, { dbh=> $dbh, basepath => $stockref->{cview_basepath}, tempfiles_subdir => $stockref->{cview_tmp_dir } }); if ($overview) { $overview->render_map(); $map_html .= $overview->get_image_html(); } } } ######################################### my $has_qtl_data = $stockref->{has_qtl_data}; my $new_pub_link = $curator || $submitter || $sequencer ? qq|Associate publication| : qq|Associate publication| ; ## EUSOL, tgrc (stock_dbxref) my $dbxrefs = $stockref->{dbxrefs}; my %source_dbs; foreach my $db_name ( keys %$dbxrefs ) { foreach my $dbxref ( @{ $dbxrefs->{$db_name} } ) { my $url = $dbxref->db->urlprefix . $dbxref->db->url; $url .= $dbxref->accession if $url ; $source_dbs{$url} = $db_name . ": " . $dbxref->accession if $url; } } my $ontology_subtitle = $curator || $submitter || $sequencer ? qq|Add ontology annotations | : qq |Add ontology annotations |; my $add_phenotype_link = $curator || $submitter || $sequencer ? qq| [Add phenotype] | : qq | [Add phenotype] |; my $edit_privs = $curator || $submitter || $sequencer; my $jbrowse_path = $c->config->{jbrowse_path}; my @path_parts = split('/', $jbrowse_path); my $basepath = $path_parts[1]; my $test_url = "/" . $basepath . "/jbrowse.conf"; my $jbrowse_url = $jbrowse_path . "%2Faccessions%2F" . $stock_id . "&tracks=DNA%2CGene%20exons%2C" . $uniquename . "_2015_V6_imputed&highlight="; my $released_variety_link = ''; if ($person_id && ($submitter || $curator || $sequencer)) { $released_variety_link = qq | |; } #line 232 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 233 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/util/import_css.mas', paths => ['/documents/inc/datatables/jquery.dataTables.css'] ); #line 233 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 235 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/util/import_javascript.mas', classes => ["bootstrap_min", "d3.d3v4Min", "jquery", "jqueryui", "jquery.dataTables-buttons-min", "thickbox", "CXGN.Page.FormattingHelpers", "jquery.cookie", "CXGN.Stock", "jquery.dataTables" ], entries => ["sequenced_accessions" ] ); #line 238 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 251 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/page_title.mas', title=> join( ': ', grep $_, ucfirst($type_name), $uniquename ) || 'Create a new stock' ); #line 251 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 254 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( { content => sub { #line 254 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '
' ); #line 262 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/form.mas', object_type=>'stock', object_id=>"$stock_id", form_name=> 'stock_form', server_side_script => '/phenome/stock/stock_ajax_form.pl', form_div_name=>'stock_details', js_object_name=> 'stockForm', page_url => "/stock/$stock_id/view/" , #alternate_new_button => 'New' alternate_new_button => '',, alternate_ghosted_new_button => '', alternate_delete_button => '', alternate_ghosted_delete_button => '' ); #line 275 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '
' ); #line 279 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($type_name eq 'accession') { #line 282 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '


' ); #line 297 "/home/production/cxgn/sgn/mason/stock/index.mas" use SGN::Image; my $schema = $stockref->{schema}; my $stock_id = $stockref->{stock_id}; my $display_image_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'selected_display_image', 'stock_property')->cvterm_id(); my $stockprop = $schema->resultset('Stock::Stockprop')->find({ stock_id => $stock_id, type_id => $display_image_cvterm_id }); if ($stockprop) { my $image_id = $stockprop->value; my $image = SGN::Image->new($schema->storage->dbh, $image_id, $c); $image_url = $image->get_image_url('small'); } else { my $image_id = $stockref->{image_ids}->[0]->[0]; my $image = SGN::Image->new($schema->storage->dbh, $image_id, $c); $image_url = $image->get_image_url('small'); } my $no_img_url = '/data/images/image_files/XX/XX/XX/XX/XXXXXXXXXXXXXXXXXXXXXXXX/small'; my $no_img_url_test = '/data/images/image_files_test/XX/XX/XX/XX/XXXXXXXXXXXXXXXXXXXXXXXX/small'; if (index($image_url, $no_img_url) != -1 || index($image_url, $no_img_url_test) != -1) { #line 320 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '

No accession image to display

' ); #line 321 "/home/production/cxgn/sgn/mason/stock/index.mas" } else { #line 324 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' print( $image_url ); #line 324 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '" class="img-responsive" style="max-width: 100%; height: auto;" /> ' ); #line 325 "/home/production/cxgn/sgn/mason/stock/index.mas" } #line 328 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '


' ); #line 332 "/home/production/cxgn/sgn/mason/stock/index.mas" } else { #line 335 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '


' ); #line 337 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/util/barcode.mas', identifier => "$identifier_prefix"."$stock_id", text=> "$identifier_prefix stock $stock_id ($uniquename)", format=>"stock_qrcode" ); #line 337 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '

' ); #line 340 "/home/production/cxgn/sgn/mason/stock/index.mas" } #line 343 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '
' ); #line 347 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( { content => sub { #line 347 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 348 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/stock/stockprops.mas', stock_id =>$stock_id, form_div_id => 'released_variety_link', props => ['released_variety_name'], div_name => 'released_variety_name', edit_privs => $edit_privs, subset => ['released_variety_name'], editable => ['released_variety_name'] ); #line 355 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 356 "/home/production/cxgn/sgn/mason/stock/index.mas" } }, '/page/info_section.mas', title => "Released variety name", subtitle=>$released_variety_link, is_subsection => 1 ); #line 356 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '
' ); #line 365 "/home/production/cxgn/sgn/mason/stock/index.mas" } }, '/page/info_section.mas', title=>"Stock details" , collapsible=>1, collapsed=>0, subtitle => " " ); #line 365 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 367 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( { content => sub { #line 367 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 369 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($type_name eq 'population') { $m->print( ' ' ); #line 370 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, type_name => $type_name, info_section_title => "

Members

", info_section_subtitle => 'View members in this population .', icon_class => "glyphicon glyphicon-list-alt", info_section_id => "population_members_section", info_section_collapsed => 0 ); #line 370 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 371 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, type_name => $type_name, info_section_title => "

Seedlot Info

", info_section_subtitle => 'View seedlot information of each member in this population .', icon_class => "glyphicon glyphicon-retweet", info_section_id => "population_seedlot_info_section", info_section_collapsed => 1 ); #line 371 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 372 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 374 "/home/production/cxgn/sgn/mason/stock/index.mas" my $subtitle = $edit_privs ? "" : ""; my $props_subtitle = $edit_privs ? "" : ""; $m->print( ' ' ); #line 377 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($type_name eq 'plot' || $type_name eq 'plant' || $type_name eq 'subplot' || $type_name eq 'tissue_sample') { $m->print( ' ' ); #line 378 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Experiment Usage

", info_section_subtitle => 'View experiments that this stock has been used in.', icon_class => "glyphicon glyphicon-leaf", info_section_id => "stock_trials_section" ); #line 378 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 379 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Related Stocks

", info_section_subtitle => 'View any accession, plot, plant, and/or tissue_sample that are linked to this stock.', icon_class => "glyphicon glyphicon-retweet", info_section_id => "stock_related_stock_section", stock_uniquename => $uniquename, type_name => $type_name ); #line 379 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 380 "/home/production/cxgn/sgn/mason/stock/index.mas" my $trait_assayed_buttons = $type_name eq 'plot' ? " $p_download_link Direct plot phenotyping" : " $p_download_link"; $m->print( ' ' ); #line 381 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Traits Assayed

", info_section_subtitle => 'View and download phenotypic data for this stock.', icon_class => "glyphicon glyphicon-equalizer", info_section_id => "stock_traits_section", buttons_html => $trait_assayed_buttons ); #line 381 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 382 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 384 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($type_name ne 'vector_construct' ){ $m->print( ' ' ); #line 385 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, type_name => $type_name, stockref => $stockref, buttons_html => $subtitle.$props_subtitle, info_section_title => "

Additional Info

", info_section_subtitle => 'View and edit additional properties such as synonyms, editors, and all types of properties.', icon_class => "glyphicon glyphicon-info-sign", info_section_id => "stock_additional_info_section", stockprops => $stockprops, edit_privs => $edit_privs, editable_stock_props => \@editable_stock_props, editor_link => $editor_link_table, source_dbs => \%source_dbs, locus_add_uri => $locus_add_uri, new_locus_link => $new_locus_link, allele_div => $allele_div, is_owner => $is_owner, info_section_collapsed => 0 ); #line 385 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 386 "/home/production/cxgn/sgn/mason/stock/index.mas" } else { $m->print( ' ' ); #line 387 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, type_name => $type_name, stockref => $stockref, buttons_html => $subtitle.$props_subtitle, info_section_title => "

Additional Info

", info_section_subtitle => 'View and edit additional properties such as synonyms, editors, and all types of properties.', icon_class => "glyphicon glyphicon-info-sign", info_section_id => "stock_additional_info_section", stockprops => $stockprops, edit_privs => $edit_privs, editable_stock_props => \@editable_vector_props, editor_link => $editor_link_table, source_dbs => \%source_dbs, locus_add_uri => $locus_add_uri, new_locus_link => $new_locus_link, allele_div => $allele_div, is_owner => $is_owner, info_section_collapsed => 1 ); #line 387 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 388 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, type_name => $type_name, stockref=> $stockref, info_section_title => "

Vector Viewer

", info_section_subtitle => "", info_section_id => "vector_view", edit_privs => $edit_privs, is_owner => $is_owner, info_section_collapsed => 0 ); #line 388 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 389 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Transgenic Line Details

", info_section_subtitle => 'View accessions (transgenic lines) containing this vector construct and number of transgene insertions.', icon_class => "glyphicon glyphicon-list-alt", info_section_id => "vector_transgenic_line_details_section", stock_uniquename => $uniquename, type_name => $type_name ); #line 389 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 390 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Obsoleted Transgenic Lines

", info_section_subtitle => 'View obsoleted accessions (transgenic lines) and metadata.', icon_class => "glyphicon glyphicon-remove", info_section_id => "vector_obsoleted_accessions_section", stock_uniquename => $uniquename, type_name => $type_name ); #line 390 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 391 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Related Transformation Info

", info_section_subtitle => 'View transformation ids related to this vector construct.', icon_class => "glyphicon glyphicon-retweet", info_section_id => "vector_related_accessions_section", stock_uniquename => $uniquename, type_name => $type_name ); #line 391 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 392 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 394 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($is_a_transgenic_line) { $m->print( ' ' ); #line 395 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', info_section_collapsed => 1, stock_id => $stock_id, info_section_title => "

Related Transformation Info

", info_section_subtitle => 'View related information about transformation experiment.', icon_class => "glyphicon glyphicon-list-alt", info_section_id => "related_transformation_info_section" ); #line 395 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 396 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 398 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($type_name eq 'accession'){ $m->print( ' ' ); #line 399 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, type_name => $type_name, info_section_title => "

Experiment Usage

", info_section_subtitle => 'View experiments that this stock has been used in.', icon_class => "glyphicon glyphicon-leaf", info_section_id => "stock_trials_section" ); #line 399 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 400 "/home/production/cxgn/sgn/mason/stock/index.mas" my $trait_assayed_buttons = $type_name eq 'plot' ? " $p_download_link Direct plot phenotyping" : " $p_download_link"; $m->print( ' ' ); #line 401 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Traits Assayed

", info_section_subtitle => 'View and download phenotypic data for this stock.', icon_class => "glyphicon glyphicon-equalizer", info_section_id => "stock_traits_section", buttons_html => $trait_assayed_buttons ); #line 401 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 402 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 404 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($type_name eq 'accession' || $type_name eq 'plant' || $type_name eq 'plot' || $type_name eq 'tissue_sample'){ $m->print( ' ' ); #line 406 "/home/production/cxgn/sgn/mason/stock/index.mas" my $sequencing_status_button = ''; if ($c->user) { $sequencing_status_button = ''; } else { $sequencing_status_button = ''; } $m->print( ' ' ); #line 414 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Sequencing Status

", info_section_subtitle => 'View and edit sequencing status info for this stock.', icon_class => "glyphicon glyphicon-inbox", info_section_id => "stock_sequencing_status_section", buttons_html => "$sequencing_status_button", map_html => $map_html ); #line 414 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 418 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Genotype Marker Data

", info_section_subtitle => 'View and download phenotypic data for this stock.', icon_class => "glyphicon glyphicon-map-marker", info_section_id => "stock_genotypes_section", map_html => $map_html ); #line 418 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 419 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 421 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($type_name eq 'accession'){ $m->print( ' ' ); #line 423 "/home/production/cxgn/sgn/mason/stock/index.mas" my $collapsible = 0; if ($has_pedigree==1) { $collapsible = 1; } my $add_parent_link = ''; if ($person_id && ($submitter || $curator || $sequencer)) { $add_parent_link = qq | |; } my $remove_parent_link = ''; if ($person_id && ($submitter || $curator || $sequencer)) { $remove_parent_link = qq | |; } #line 434 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 435 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Pedigree

", info_section_subtitle => 'View and edit pedigree information.', icon_class => "glyphicon glyphicon-random", info_section_id => "stock_pedigree_section", buttons_html => $add_parent_link.$remove_parent_link, has_pedigree => $has_pedigree, info_section_collapsed => 1 ); #line 435 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 436 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Related Stocks

", info_section_subtitle => 'View any plots, plants, tissue_sample, and/or accessions that are linked to this stock.', icon_class => "glyphicon glyphicon-retweet", info_section_id => "stock_related_stock_section", stock_uniquename => $uniquename, type_name => $type_name ); #line 436 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 438 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 440 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Images

", info_section_subtitle => 'View and add images of this stock and of related stocks.', icon_class => "glyphicon glyphicon-camera", info_section_id => "stock_images_section", image_ids => $image_ids, related_image_ids => $related_image_ids, dbh => $dbh, curator =>$curator, buttons_html => qq|Add new imageCompare Images| ); #line 440 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 442 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Upload Data Files

", info_section_subtitle => 'Upload any additional files for this Accession.', icon_class => "glyphicon glyphicon-cloud-upload", info_section_id => "stock_upload_files" ); #line 442 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 444 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Literature Annotation

", info_section_subtitle => 'View annotations for this stock found in literatur and ontologies.', icon_class => "glyphicon glyphicon-book", info_section_id => "stock_literature_annotation_section", buttons_html => $new_pub_link.$ontology_subtitle, pubs => $pubs, cvterm_add_uri => $cvterm_add_uri, stockref => $stockref, trait_ontology_db_name => $trait_ontology_db_name, is_owner => $is_owner, dbh=>$dbh ); #line 444 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 446 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

JBrowse Genome Alignments

", info_section_subtitle => 'View JBrowse tracks for this stock.', icon_class => "glyphicon glyphicon-align-left", info_section_id => "stock_jbrowse_section" ); #line 446 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 448 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Comments

", info_section_subtitle => 'View and add comments to this stock.', icon_class => "glyphicon glyphicon-pencil", info_section_id => "stock_comments_section", referer => $this_page ); #line 448 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 450 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, info_section_title => "

Audit Table

", info_section_subtitle => 'Track audit information for this stock.', icon_class => "glyphicon glyphicon-time", info_section_id => "audit_table_section", stock_uniquename => $uniquename, referer => $this_page ); #line 450 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 452 "/home/production/cxgn/sgn/mason/stock/index.mas" if ($edit_privs && $type_name eq 'population') { $m->print( ' ' ); #line 453 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, stock_uniquename => $uniquename, info_section_title => "

Delete This Stock

", info_section_subtitle => 'Delete this population.', icon_class => "glyphicon glyphicon-trash", info_section_id => "population_delete_section" ); #line 453 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 454 "/home/production/cxgn/sgn/mason/stock/index.mas" } elsif ($edit_privs && $type_name ne 'population') { $m->print( ' ' ); #line 455 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/page/detail_page_2_col_section.mas', stock_id => $stock_id, stock_uniquename => $uniquename, is_obsolete=> $is_obsolete, is_in_trial=> $is_in_trial, info_section_title => "

" . ($is_obsolete ? "Un-Obsolete This Stock" : "Obsolete This Stock") . "

", info_section_subtitle => ($is_obsolete ? "Make a stock not obsolete so that it does show in searches" : "Make a stock obsolete so that it does not show in searches"), icon_class => "glyphicon glyphicon-trash", info_section_id => "stock_delete_section" ); #line 455 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 456 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 458 "/home/production/cxgn/sgn/mason/stock/index.mas" } }, '/page/info_section.mas', title => "Navigator" , collapsible=> 1, collapsed=>0 ); #line 458 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 460 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/stock/download_stock_phenotypes_dialog.mas', stock_id => $stock_id, stock_name => $uniquename, stock_type => $type_name ); #line 460 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '
Remove a parent (this will only remove the link to the parent, not the parent accession itself).

[loading parent list...]
' ); #line 469 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( { content => sub { #line 469 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 470 "/home/production/cxgn/sgn/mason/stock/index.mas" foreach my $project (keys %$direct_phenotypes) { my $rs = $direct_phenotypes->{$project} ; $m->print( ' ' ); #line 473 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( { content => sub { #line 479 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 480 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/stock/add_phenotype.mas', stock_id => $stock_id , trait_ontology_db_name => $trait_ontology_db_name, project=>$project ); #line 484 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 485 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/phenotypes/phenotype_data.mas', phenotypes=> $rs ); #line 487 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 488 "/home/production/cxgn/sgn/mason/stock/index.mas" } }, '/page/info_section.mas', id => "stock_phenotype", title =>"Experiment: $project", subtitle => $add_phenotype_link, is_subsection => 1, collapsible => 1 ); #line 488 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 489 "/home/production/cxgn/sgn/mason/stock/index.mas" } $m->print( ' ' ); #line 491 "/home/production/cxgn/sgn/mason/stock/index.mas" foreach my $key (keys %$members_phenotypes) { my $m_rs = $members_phenotypes->{$key}; $m->comp( { content => sub { #line 498 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 499 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/phenotypes/phenotype_data.mas', phenotypes => $m_rs, object_id => $stock_id, has_qtl => $has_qtl_data, ); #line 503 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 504 "/home/production/cxgn/sgn/mason/stock/index.mas" } }, '/page/info_section.mas', title => "Member phenotypes", subtitle => $key, is_subsection => 1, collapsible => 1, ); #line 504 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); #line 505 "/home/production/cxgn/sgn/mason/stock/index.mas" } } }, '/page/info_section.mas', title=>"Phenotype data " , subtitle=>$p_download_link , collapsible => 1, collapsed => 1 ); #line 506 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( '
TraitAverageStd devCount
' ); #line 516 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->comp( '/transformation/obsolete_stock_dialog.mas' ); #line 516 "/home/production/cxgn/sgn/mason/stock/index.mas" $m->print( ' ' ); ;return; }, 'declared_args' => { '$barcode_tempdir' => { default => ' undef' }, '$barcode_tempuri' => { default => ' undef' }, '$cvterm_add_uri' => { default => ' \'\'' }, '$cvterm_autocomplete_uri' => { default => ' undef' }, '$identifier_prefix' => { default => ' \'SGN\'' }, '$image' => { default => ' undef' }, '$image_url' => { default => ' undef' }, '$locus_add_uri' => { default => ' \'\'' }, '$locus_autocomplete_uri' => { default => ' undef' }, '$organism_autocomplete_uri' => { default => ' \'/ajax/organism/autocomplete/\'' }, '$stock_row' => { default => undef }, '$stockref' => { default => ' undef' } }, 'load_time' => 1763448494, ) ;