mason/page/detail_page_2_col_section.mas

   1 <%args>
   2 $trial_id => undef
   3 $trial_name => undef
   4 $stock_id => undef
   5 $stock_uniquename => undef
   6 $col1_width_class => "col-sm-1"
   7 $col2_width_class => "col-sm-11"
   8 $icon_class => "glyphicon glyphicon-th"
   9 $info_section_collapsible => 1
  10 $info_section_collapsed => 1
  11 $info_section_id => "2col_id"
  12 $info_section_title => "A title"
  13 $info_section_subtitle => "A subtitle"
  14 $buttons_html => undef
  15 $locations_by_program_json => undef
  16
  17 #Specific to trial detail page
  18 $has_plant_entries => undef
  19 $has_subplot_entries => undef
  20 $has_tissue_sample_entries => undef
  21 $has_expression_atlas => undef
  22 $expression_atlas_url => undef
  23 $site_project_name => undef
  24 $sgn_session_id => undef
  25 $user_name => undef
  26 $main_production_site_url => undef
  27 $trial_phenotype_files => undef
  28 $hidap_enabled => undef
  29 $location_name => undef
  30 $breeding_program_name => undef
  31 $breeding_program_id => undef
  32 $year => undef
  33 $trial_type => undef
  34 $design_name => undef
  35 $planting_date => undef
  36 $harvest_date => undef
  37 $trial_description => undef
  38 $folder_name => undef
  39 $folder_id => undef
  40 $plot_width => undef
  41 $plot_length => undef
  42 $field_size => undef
  43 $field_trial_is_planned_to_be_genotyped => undef
  44 $field_trial_is_planned_to_cross => undef
  45 $identifier_prefix => undef
  46 $genotyping_facility => undef
  47 $management_factor_date => undef
  48 $management_factor_type => undef
  49
  50 #Specific to stock detail page
  51 $type_name => undef
  52 $stockref => {}
  53 $stockprops => undef
  54 $edit_privs => undef
  55 $editable_stock_props => undef
  56 $editor_link => undef
  57 $source_dbs => {}
  58 $locus_add_uri => undef
  59 $new_locus_link => undef
  60 $allele_div => undef
  61 $is_owner => undef
  62 $map_html => undef
  63 $has_pedigree => undef
  64 $image_ids => undef
  65 $related_image_ids => undef
  66 $dbh => undef
  67 $trait_ontology_db_name => undef
  68 $pubs => undef
  69 $cvterm_add_uri => undef
  70 $referer => undef
  71
  72 #Specific to genotyping protocol detail page
  73 $protocol_id => undef
  74 $protocol_name => undef
  75 $protocol_description => undef
  76 $marker_names => []
  77 $header_information_lines => []
  78 $reference_genome_name => undef
  79 $species_name => undef
  80 $create_date => undef
  81 $sample_observation_unit_type_name => undef
  82
  83 </%args>
  84
  85 <div class="row">
  86     <div class="col-sm-12">
  87         <div class="well">
  88             <div class="row">
  89                 <div class="<% $col1_width_class %>">
  90                     <span style="font-size:3.5em;" class="<% $icon_class %>"></span>
  91                 </div>
  92                 <div class="<% $col2_width_class %>">
  93
  94                     <&| /page/info_section.mas, id => $info_section_id, title => $info_section_title, collapsible=>$info_section_collapsible, collapsed => $info_section_collapsed, subtitle=> $info_section_subtitle &>
  95
  96 % if ($buttons_html){
  97                         <div class="panel panel-default">
  98                             <div class="panel-body">
  99                                 <% $buttons_html %>
 100                             </div>
 101                         </div>
 102 % }
 103
 104                         <div class="panel panel-default">
 105                             <div class="panel-body">
 106
 107 % if ($info_section_id eq 'pheno_heatmap'){
 108                                 <& /breeders_toolbox/trial/phenotype_heatmap.mas, trial_id => $trial_id &>
 109 % } #End pheno_heatmap
 110 % if ($info_section_id eq 'trial_design_section'){
 111                                 <& /breeders_toolbox/trial/design_section.mas, trial_id => $trial_id, trial_name => $trial_name, has_subplot_entries => $has_subplot_entries, has_plant_entries => $has_plant_entries, has_tissue_sample_entries => $has_tissue_sample_entries, design_name => $design_name &>
 112 % } #End trial_design_section
 113 % if ($info_section_id eq 'trial_detail_traits_assayed'){
 114
 115 % if ($has_expression_atlas) {
 116                                 <& /breeders_toolbox/trial/export_trial_to_expression_atlas.mas, trial_id => $trial_id, trial_name=>$trial_name, expression_atlas_url=>$expression_atlas_url, site_project_name=>$site_project_name, sgn_session_id=>$sgn_session_id, user_name=>$user_name, main_production_site_url=>$main_production_site_url &>
 117 % }
 118
 119                                 <& /breeders_toolbox/trial/phenotype_summary.mas, trial_id => $trial_id &>
 120
 121 % } #End trial_detail_traits_assayed
 122 % if ($info_section_id eq 'compute_derived_traits'){
 123                                 <& /breeders_toolbox/trial/derived_trait.mas, trial_id => $trial_id &>
 124 % } #End compute_derived_traits
 125 % if ($info_section_id eq 'trial_upload_files'){
 126                                 <& /breeders_toolbox/trial/files_section.mas, trial_id => $trial_id, trial_phenotype_files => $trial_phenotype_files &>
 127 % } #End trial_upload_files
 128 % if ($info_section_id eq 'trial_analysis_tools'){
 129                                 <!-- Phenotypic correlation analysis -->
 130                                 <& /solgs/population/correlation.mas,
 131                                     trial_id => $trial_id
 132                                 &>
 133
 134                                 <& /solgs/anova/analysis.mas,
 135                                     trial_id => $trial_id
 136                                 &>
 137
 138                                 <!-- Population structure analysis PCA -->
 139                                 <& /solgs/pca/analysis.mas,
 140                                     trial_id => $trial_id
 141                                   &>
 142
 143                                 <!-- Clustering -->
 144                                 <& /solgs/cluster/analysis.mas,
 145                                     trial_id => $trial_id
 146                                 &>
 147
 148 % if ($hidap_enabled) {
 149                                 <& /hidap/hidap_trial_link.mas, main_production_site_url=>$main_production_site_url, program => $breeding_program_name, folder => $folder_name, trial => $trial_name &>
 150 % }
 151 % } #End trial_analysis_tools
 152 % if ($info_section_id eq 'trial_weather_data'){
 153                                 <& /breeders_toolbox/trial/weather.mas, location => $location_name &>
 154 % } #End trial_weather_data
 155 % if ($info_section_id eq 'trial_jbrowse_data'){
 156                                 <& /breeders_toolbox/trial/jbrowse_instance.mas, trial_id => $trial_id &>
 157 %} #End trial_jbrowse_data
 158 % if ($info_section_id eq 'trial_linkage_section'){
 159                                 <&| /page/info_section.mas, title => 'Field Trial to Field Trial Linkage', id => 'field_trial_from_field_trial_section', collapsible => 1, collapsed => 1 &>
 160                                     <& /breeders_toolbox/trial/field_trial_from_field_trial_linkage.mas, trial_id => $trial_id &>
 161                                 </&>
 162                                 <&| /page/info_section.mas, title => 'Field Trial to Genotyping Plate Linkage', id => 'genotyping_trial_from_field_trial_section', collapsible => 1, collapsed => 1 &>
 163                                     <& /breeders_toolbox/trial/genotyping_trial_from_field_trial_linkage.mas, trial_id => $trial_id, trial_type => 'field_trial' &>
 164                                 </&>
 165                                 <&| /page/info_section.mas, title => 'Field Trial to Crossing Experiment Linkage', id => 'crossing_trial_from_field_trial_section', collapsible => 1, collapsed => 1 &>
 166                                     <& /breeders_toolbox/trial/crossing_trial_from_field_trial_linkage.mas, trial_id => $trial_id, trial_type => 'field_trial' &>
 167                                 </&>
 168 %} #End trial_linkage_section
 169 % if ($info_section_id eq 'trial_deletion_section'){
 170                                 <&| /page/info_section.mas, title=>'Delete trial data', subtitle=>'<font color="red" role="">Deletion cannot be undone</font>', collapsed=>1, collapsible=>1 &>
 171                                     <& /breeders_toolbox/trial/trial_deletion.mas, trial_id => $trial_id  &>
 172                                 </&>
 173 %} #End trial_deletion_section
 174 % if ($info_section_id eq 'trial_data_agreement_section'){
 175                                 <& /breeders_toolbox/data_agreement.mas, trial_id => $trial_id &>
 176 % } #End trial_data_agreement_section
 177
 178 % if ($info_section_id eq 'stock_additional_info_section'){
 179                                 <& /stock/additional_info_section.mas, stock_id => $stock_id, type_name => $type_name, stockprops => $stockprops, edit_privs => $edit_privs, editable_stock_props => $editable_stock_props, editor_link => $editor_link, source_dbs => $source_dbs, locus_add_uri => $locus_add_uri, allele_div => $allele_div, is_owner => $is_owner &>
 180 % } #End stock_additional_info_section
 181 % if ($info_section_id eq 'stock_trials_section'){
 182                                 <& /stock/trials.mas, stock_id => $stock_id &>
 183 % } #End stock_trials_section
 184 % if ($info_section_id eq 'stock_traits_section'){
 185                                 <& /stock/traits.mas, stock_id => $stock_id &>
 186 % } #End stock_traits_section
 187 % if ($info_section_id eq 'stock_genotypes_section'){
 188                                 <& /stock/direct_genotypes.mas, stock_id => $stock_id, map_html => $map_html &>
 189 % } #End stock_genotypes_section
 190 % if ($info_section_id eq 'stock_pedigree_section'){
 191                                 <&| /page/info_section.mas, title=>"Pedigree and Descendants" , collapsible=> 1, collapsed=>0 &>
 192                                     <& /pedigree/stock_pedigree.mas, stock_id => $stock_id, has_pedigree => $has_pedigree &>
 193                                 </&>
 194
 195                                 <& /pedigree/stock_pedigree_string.mas, stock_id => $stock_id &>
 196 % } #End stock_pedigree_section
 197 % if ($info_section_id eq 'stock_related_stock_section'){
 198                                 <& /stock/related_stock.mas, stock_id => $stock_id, stock_uniquename => $stock_uniquename, stock_type => $type_name &>
 199 % } #End stock_related_stock_section
 200 % if ($info_section_id eq 'stock_images_section'){
 201                                 <&| /page/info_section.mas, title=>"Images of This Stock(" .  scalar(@$image_ids)  . ")", collapsible=>1, collapsed=>0 &>
 202                                     <& /image/print_images.mas , images=>$image_ids , dbh=>$dbh, additional_image_button_id=>'stock_images' &>
 203                                 </&>
 204
 205                                 <&| /page/info_section.mas, title=>"Images of Related Stock(s) (" .  scalar(@$related_image_ids)  . ")", collapsible=>1, collapsed=>0 &>
 206                                     <& /image/print_images.mas , images=>$related_image_ids , dbh=>$dbh, additional_image_button_id=>'related_stock_images' &>
 207                                 </&>
 208 % } #End stock_images_section
 209 % if ($info_section_id eq 'stock_sequencing_status_section'){
 210                                 <& /stock/sequencing_status.mas, stock_id => $stock_id &>
 211 % } #End stock requencing status section
 212 % if ($info_section_id eq 'stock_literature_annotation_section'){
 213                                 <&| /page/info_section.mas, title=>"Literature annotation (".scalar( @$pubs ).")" , id=>"publications" , collapsible=>1, collapsed=>1 &>
 214
 215
 216 % foreach my $publication ( @$pubs  ) {
 217   <& /chado/publication.mas, pub=>$publication &>
 218     <br >
 219 % }
 220
 221                                 </&>
 222
 223                                 <&| /page/info_section.mas, id   => 'stock_ontology', title=>"Ontology annotation (" . $stockref->{ontology_count} . ")" &>
 224                                     <& /ontology/associate_ontology.mas,
 225                                     trait_db_name => $trait_ontology_db_name,
 226                                     object_id     => $stock_id ,
 227                                     object_name   => "stock",
 228                                     cvterm_add_uri=> $cvterm_add_uri,
 229                                     ontology_url  => "/stock/$stock_id/ontologies/",
 230                                     reference_uri => "/stock/$stock_id/references/",
 231                                     evidence_with_uri => "/stock/$stock_id/evidences/",
 232                                     show_form     => $is_owner  &>
 233                                 </&>
 234 % } #End stock_literature_annotation_section
 235 % if ($info_section_id eq 'stock_jbrowse_section'){
 236                                 <p id="jbrowse_check">[loading...]</p>
 237 % } #End stock_jbrowse_section
 238 % if ($info_section_id eq 'stock_comments_section'){
 239                                 <& /page/comments.mas, object_type=>'stock', object_id=>$stock_id, referer=>$referer &>
 240 % } #End stock_comments_section
 241 % if ($info_section_id eq 'stock_delete_section'){
 242                                 <& /stock/delete.mas, stock_id=>$stock_id &>
 243 % } #End stock_delete_section
 244
 245
 246 % if ($info_section_id eq 'manage_tissue_samples_field_trials'){
 247                                 <& /breeders_toolbox/tissue_samples/field_trials_with_tissue_samples.mas &>
 248 % } #End manage_tissue_samples_field_trials
 249 % if ($info_section_id eq 'manage_tissue_samples_genotyping_trials'){
 250                                 <& /breeders_toolbox/tissue_samples/genotyping_trials.mas &>
 251 % } #End manage_tissue_samples_genotyping_trials
 252 % if ($info_section_id eq 'trial_details'){
 253                                 <& /breeders_toolbox/trial/trial_details.mas, trial_id=>$trial_id, trial_name=>$trial_name, breeding_program_name=>$breeding_program_name, breeding_program_id=>$breeding_program_id, location_name=>$location_name, year=>$year, trial_type=>$trial_type, planting_date=>$planting_date, harvest_date=>$harvest_date, trial_description=>$trial_description, folder_name=>$folder_name, folder_id=>$folder_id, identifier_prefix=>$identifier_prefix, plot_width=>$plot_width, plot_length=>$plot_length, field_size=>$field_size, field_trial_is_planned_to_be_genotyped=>$field_trial_is_planned_to_be_genotyped, field_trial_is_planned_to_cross=>$field_trial_is_planned_to_cross &>
 254 % } #End trial_details
 255 % if ($info_section_id eq 'stocks_search_graphical_filtering'){
 256                                 <& /search/stocks_graphicalfiltering.mas &>
 257 % } #End stocks_search_graphical_filtering
 258 % if ($info_section_id eq 'genotyping_data_project_details'){
 259                                 <& /breeders_toolbox/genotyping_data_project/details.mas, trial_id=>$trial_id, trial_name=>$trial_name, breeding_program_name=>$breeding_program_name, breeding_program_id=>$breeding_program_id, location_name=>$location_name, year=>$year, trial_description=>$trial_description, identifier_prefix=>$identifier_prefix, genotyping_facility => $genotyping_facility &>
 260 % } #End genotyping_data_project_details
 261 % if ($info_section_id eq 'genotyping_data_project_protocols'){
 262                                 <& /breeders_toolbox/genotyping_data_project/protocols.mas, trial_id=>$trial_id &>
 263 % } #End genotyping_data_project_protocols
 264 % if ($info_section_id eq 'genotyping_data_project_data'){
 265                                 <& /breeders_toolbox/genotyping_data_project/genotype_data.mas, trial_id=>$trial_id &>
 266 % } #End genotyping_data_project_data
 267 % if ($info_section_id eq 'identifier_generation_list'){
 268                                 <& /breeders_toolbox/identifier_generation/list_identifier_generation.mas &>
 269 % } #End identifier_generation_list
 270 % if ($info_section_id eq 'management_factor_details'){
 271                                 <& /breeders_toolbox/trial/management_factor_details.mas, trial_id=>$trial_id, trial_name=>$trial_name, year=>$year, management_factor_type=>$management_factor_type, management_factor_date=>$management_factor_date &>
 272 % } #End management_factor_details
 273 % if ($info_section_id eq 'management_factor_design'){
 274                                 <& /breeders_toolbox/trial/design_section_management_factor.mas, trial_id => $trial_id, trial_name => $trial_name, has_subplot_entries => $has_subplot_entries, has_plant_entries => $has_plant_entries, has_tissue_sample_entries => $has_tissue_sample_entries, design_name => $design_name &>
 275 % } #End management_factor_design
 276
 277 % if ($info_section_id eq 'genotyping_protocol_details'){
 278                                 <& /breeders_toolbox/genotyping_protocol/details.mas, protocol_id => $protocol_id, protocol_name => $protocol_name, protocol_description => $protocol_description, marker_names => $marker_names, header_information_lines => $header_information_lines, reference_genome_name => $reference_genome_name, species_name => $species_name, create_date => $create_date, sample_observation_unit_type_name => $sample_observation_unit_type_name &>
 279 % } #End genotyping_protocol_details
 280 % if ($info_section_id eq 'genotyping_protocol_markers'){
 281                                 <& /breeders_toolbox/genotyping_protocol/markers.mas, protocol_id => $protocol_id &>
 282 % } #End genotyping_protocol_markers
 283 % if ($info_section_id eq 'genotyping_protocol_genotype_data'){
 284                                 <& /breeders_toolbox/genotyping_protocol/genotype_data.mas, protocol_id => $protocol_id &>
 285 % } #End genotyping_protocol_genotype_data
 286
 287 % if ($info_section_id eq 'crossingtrial_details'){
 288                                 <& /breeders_toolbox/cross/crossingtrial_details.mas, trial_id=>$trial_id, trial_name=>$trial_name, breeding_program_name=>$breeding_program_name, location_name=>$location_name, year=>$year, planting_date=>$planting_date, harvest_date=>$harvest_date, trial_description=>$trial_description, folder_name=>$folder_name, folder_id=>$folder_id, identifier_prefix=>$identifier_prefix &>
 289 % } #End crossingtrial_details
 290
 291 % if ($info_section_id eq 'crosses_in_crossingtrial_section'){
 292                                 <& /breeders_toolbox/cross/crosses_in_crossingtrial.mas, trial_id=>$trial_id &>
 293 % } #End crosses_in_crossingtrial_section
 294
 295 % if ($info_section_id eq 'cross_properties_crossingtrial_section'){
 296                                 <& /breeders_toolbox/cross/cross_properties_crossingtrial.mas, trial_id=>$trial_id &>
 297 % } #End cross_properties_crossingtrial_section
 298
 299 % if ($info_section_id eq 'progenies_in_crossingtrial_section'){
 300                                 <& /breeders_toolbox/cross/progenies_in_crossingtrial.mas, trial_id=>$trial_id &>
 301 % } #End progenies_in_crossingtrial_section
 302
 303 % if ($info_section_id eq 'seedlots_from_crossingtrial_section'){
 304                                 <& /breeders_toolbox/cross/seedlots_from_crossingtrial.mas, trial_id=>$trial_id, breeding_program_name=>$breeding_program_name, breeding_program_id=>$breeding_program_id, locations_by_program_json=>$locations_by_program_json &>
 305 % } #End seedlots_from_crossingtrial_section
 306
 307 % if ($info_section_id eq 'crossing_trial_from_field_trial_section'){
 308                                 <& /breeders_toolbox/trial/crossing_trial_from_field_trial_linkage.mas, trial_id => $trial_id, trial_type => 'crossing_trial' &>
 309 % } #End crossing_trial_from_field_trial_section
 310
 311 % if ($info_section_id eq 'crossing_experiment_deletion_section'){
 312                                 <& /breeders_toolbox/cross/crossing_experiment_deletion.mas, trial_id => $trial_id  &>
 313 %} #End crossing_experiment_deletion_section
 314
 315 % if ($info_section_id eq 'manage_drone_imagery_main'){
 316                                 <& /breeders_toolbox/drone_imagery/raw_image_section.mas &>
 317 % } #End manage_drone_imagery_main
 318
 319 % if ($info_section_id eq 'manage_drone_imagery_generate_plot_polygons_section'){
 320                                 <& /breeders_toolbox/drone_imagery/generate_plot_polygons_section.mas &>
 321 % } #End manage_drone_imagery_generate_plot_polygons_section
 322 % if ($info_section_id eq 'manage_drone_imagery_standard_process_generate_plot_polygons_section'){
 323                                 <& /breeders_toolbox/drone_imagery/generate_plot_polygons_standard_process_section.mas &>
 324 % } #End manage_drone_imagery_generate_plot_polygons_section
 325
 326 % if (!$info_section_id){
 327                                 <p>No section specified! Main content goes here!</p>
 328 % }
 329
 330                             </div>
 331                         </div>
 332                     </&>
 333                 </div>
 334             </div>
 335         </div>
 336     </div>
 337 </div>