Merge pull request #3550 from solgenomics/topic/acronyms_display

adds trait acronyms legend in trial detail page

js/source/legacy/solGS/loadAcronyms.js

@@ -0,0 +1,70 @@
+/**
+* trait acronyms loader
+* Isaak Y Tecle <[email protected]>
+*
+*/
+
+
+var solGS = solGS || function solGS () {};
+
+solGS.acronyms = {
+
+    loadAcronyms: function() {
+       var id;
+       var page = document.URL;
+
+       if (page.match(/breeders\/trial\//)) {
+           id = jQuery('#trial_id').val();
+       } else {
+          id = jQuery('#training_pop_id').val();
+       }
+
+       var acros = jQuery.ajax({
+            type    : 'POST',
+            dataType: 'json',
+            data    : {'id': id},
+            url     : '/solgs/load/trait/acronyms/',
+        });
+
+        return acros;
+    },
+
+
+    displayAcronyms: function(data) {
+
+        var table = jQuery('#trait_acronyms_table').DataTable({
+        'searching' : false,
+        'ordering'  : false,
+        'processing': true,
+        'paging'    : false,
+        'info'      : false,
+        });
+
+        table.rows.add(data).draw();
+
+    }
+
+/////////////
+}
+////////////
+
+
+jQuery(document).ready( function() {
+    console.log('loading acronyms....')
+
+    jQuery('#trait_acronyms_div').show();
+
+    solGS.acronyms.loadAcronyms().done( function(res) {
+        solGS.acronyms.displayAcronyms(res.acronyms);
+    });
+
+    solGS.acronyms.loadAcronyms().fail( function(res) {
+         jQuery('#trait_acronyms_table').hide();
+        var errorMsg = 'Error occured loading acronyms';
+        jQuery('#acronyms_message')
+            .html(errorMsg)
+            .show()
+            .fadeOut(50000);
+    });
+
+});

lib/SGN/Controller/solGS/Correlation.pm

@@ -17,6 +17,8 @@ use JSON;
 use Try::Tiny;
 use Scalar::Util qw /weaken reftype/;
 use Storable qw/ nstore retrieve /;
+
+
 BEGIN { extends 'Catalyst::Controller' }
 
 
@@ -103,12 +105,14 @@ sub correlation_genetic_data :Path('/correlation/genetic/data/') Args(0) {
     $c->stash->{pop_id}   = $model_id;
     $c->stash->{training_pop_id} = $model_id;
     $c->stash->{training_traits_ids} = \@traits_ids;
+
     $c->stash->{selection_pop_id} = $corr_pop_id if $pop_type =~ /selection/;
 
     #$c->controller('solGS::Files')->selection_index_file($c);
 
     # $c->controller('solGS::TraitsGebvs')->combine_gebvs_of_traits($c);
     $c->controller('solGS::TraitsGebvs')->run_combine_traits_gebvs($c);
+
     my $combined_gebvs_file = $c->stash->{combined_gebvs_file};
     my $tmp_dir = $c->stash->{correlation_temp_dir};
     $combined_gebvs_file = $c->controller('solGS::Files')->copy_file($combined_gebvs_file, $tmp_dir);
@@ -237,6 +241,7 @@ sub genetic_correlation_output_files {
     my $type         = $c->stash->{type};
 
     my $selection_pop_id = $c->stash->{selection_pop_id};
+
     $model_id    = $c->stash->{model_id};
     my $identifier  =  $type =~ /selection/ ? $model_id . "_" . $corre_pop_id :  $corre_pop_id;
 
@@ -271,7 +276,7 @@ sub pheno_correlation_analysis_output :Path('/phenotypic/correlation/analysis/ou
 
     if (-s $corre_json_file)
     {
-	$ret->{acronyms} =  $self->trait_acronyms($c);
+	# $ret->{acronyms} =  $self->trait_acronyms($c);
         $ret->{status}   = 'success';
         $ret->{data}     = read_file($corre_json_file, {binmode => ':utf8'});
     }

lib/SGN/Controller/solGS/TraitsGebvs.pm

@@ -45,16 +45,16 @@ sub combine_gebvs_jobs_args {
             write_file($gebvs_files, {append => 1, binmode => ':utf8'}, "\t". $index_file)
         }
 
-        my $identifier = $self->combined_gebvs_file_id($c);
-	    my $tmp_dir = $c->stash->{solgs_tempfiles_dir};
-        $self->combined_gebvs_file($c);
-        my $combined_gebvs_file = $c->stash->{combined_gebvs_file};
+	my $identifier = $self->combined_gebvs_file_id($c);	
+	my $tmp_dir = $c->stash->{solgs_tempfiles_dir};
+	
+        my $combined_gebvs_file = $c->controller('solGS::Files')->create_tempfile($tmp_dir, "combined_gebvs_${identifier}");
 
         $c->stash->{input_files}  = $gebvs_files;
         $c->stash->{output_files} = $combined_gebvs_file;
         $c->stash->{r_temp_file}  = "combining-gebvs-${identifier}";
         $c->stash->{r_script}     = 'R/solGS/combine_gebvs_files.r';
-	    $c->stash->{analysis_tempfiles_dir} = $tmp_dir;
+	$c->stash->{analysis_tempfiles_dir} = $tmp_dir;
     }
     else
     {
@@ -126,7 +126,6 @@ sub get_gebv_files_of_traits {
     my $training_pop_id = $c->stash->{training_pop_id} || $c->stash->{combo_pops_id} || $c->stash->{corre_pop_id};
     $c->stash->{model_id} = $training_pop_id;
     my $selection_pop_id = $c->stash->{selection_pop_id};
-
     my $dir = $c->stash->{solgs_cache_dir};
 
     my $gebv_files;
@@ -276,6 +275,24 @@ sub create_traits_selection_id {
 
 
 
+sub load_acronyms: Path('/solgs/load/trait/acronyms') Args() {
+    my ($self, $c) = @_;
+
+   my $id = $c->req->param('id');
+   $c->controller('solGS::solGS')->get_all_traits($c, $id);
+   my $acronyms = $c->controller('solGS::solGS')->get_acronym_pairs($c, $id);
+
+   my $ret->{acronyms}  = $acronyms;
+   my $json = JSON->new();
+   $ret = $json->encode($ret);
+
+   $c->res->content_type('application/json');
+   $c->res->body($ret);
+
+}
+
+
+
 #####
 
 

lib/SGN/Controller/solGS/solGS.pm

@@ -1540,7 +1540,7 @@ sub get_all_traits {
     if (!-s $traits_file)
     {
 	my $page = $c->req->path;
-	if ($page =~ /solgs\/population\/|anova\/|correlation\// && $pop_id !~ /\D+/)
+	if ($page =~ /solgs\/population\/|anova\/|correlation\/|acronyms/ && $pop_id !~ /\D+/)
 	{
 	    $self->save_single_trial_traits($c, $pop_id);
 	}

mason/page/detail_page_2_col_section.mas

@@ -199,6 +199,10 @@ $sampling_facilities => ()
                                     trial_id => $trial_id
                                 &>
 
+                                <& /solgs/population/trait_acronyms.mas,
+                                  trial_id => $trial_id
+                              &>
+
 % if ($c->req->base =~ /sweetpotatobase/) {
                                 <& /tools/qualityControl/qualityControl.mas,
                                     trial_id => $trial_id

mason/solgs/population.mas

@@ -95,9 +95,7 @@ $training_pop_id = $pop_id;
 
 %}
 
-  <& population/acronym.mas,
-   acronym => $acronym,
-    &>
+  <& /solgs/population/trait_acronyms.mas &>
 
 %} else {
 
@@ -107,7 +105,7 @@ $training_pop_id = $pop_id;
       title       => "Genotype Data"
 &>
 
-  <div id="traits_list_message"  style="font-weight:bold;text-align:center;text-transform:uppercase;color:#A7C942">
+  <div id="traits_list_message"  class="message">
     <p>There is no genotype data for this population.</p>
   </div>
 

mason/solgs/population/trait_acronyms.mas

@@ -0,0 +1,53 @@
+<%doc>
+
+=head1 NAME
+
+/solgs/population/acronym.mas -- displays a list of traits and their acronyms.
+
+=AUTHOR
+
+Isaak Y Tecle ([email protected])
+
+=cut
+
+</%doc>
+
+<%args>
+
+$trial_id => undef;
+$training_pop_id => undef;
+
+</%args>
+
+<%perl>
+</%perl>
+
+
+<& /util/import_javascript.mas, classes => ["solGS.loadAcronyms", "jquery.dataTables"] &>
+
+<&| /page/info_section.mas,
+    collapsible => 1,
+    collapsed   => 1,
+    title       => "Acronyms legend",
+  &>
+
+
+  <div id="trait_acronyms_div" style="display:none">
+    <div id="acronyms_message"  class="message"></div>
+
+      <table class="table" id="trait_acronyms_table" style="text-align: left;">
+        <thead>
+          <tr>
+        	<th>Acronym</th>
+            <th>Trait</th>
+          </tr>
+        </thead>
+      </table>
+
+      <input type="hidden" id="trial_id" value="<% $trial_id %>" />
+
+</div>
+
+
+
+</&>