Add newick download to species tree; Remove unwanted text

aparton · Jul 27, 2017 · 95cd208 · 95cd208
1 parent 7f72f04
commit 95cd208
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Showing 4 changed files with 17 additions and 12 deletions.
diff --git a/widgets/htdocs/components/95_speciestree.css b/widgets/htdocs/components/95_speciestree.css
@@ -24,7 +24,7 @@ div.js_tree div.toolbar_menu div.current        { background: url("/i/16/rev/che
 div.toolbar_menu div.header                     { cursor: auto; }
 div.tree_menu, div.resize_menu, div.filter_menu { display: none; }
 div.js_tree div.resize                          { background-image: url("/i/16/rev/image_resize.png"); cursor: pointer; float: left; height: 16px; margin: 0 4px 2px; width: 16px; }
-div.js_tree div.export                          { background-image: url("/i/16/rev/picture.png"); cursor: pointer; float: left; height: 16px; margin: 0 4px 2px; width: 16px; }
+div.js_tree div.export                          { background-image: url("/i/16/rev/download.png"); cursor: pointer; float: left; height: 16px; margin: 0 4px 2px; width: 16px; }
 div .tnt_tooltip                                { background-color: #eaeeff; border: 1px solid #eaeeff; box-shadow: 5px 5px 15px #666; font-size: 10px; font-weight: bold; opacity: 0.94; padding: 0px; text-align: left; white-space: normal; width: 210px; position: absolute !important; }
 .tnt_zmenu                                      { width: 210px; border-style: none;}
 .tnt_zmenu_header                               { background-color: #667aa6; }

diff --git a/widgets/htdocs/info/about/speciestree.html b/widgets/htdocs/info/about/speciestree.html
@@ -10,9 +10,6 @@ <h1>Species Tree</h1>
 <p>
 The species tree is maintained by the <a href="/info/genome/compara/">Compara team</a>
 (more information <a href="/info/genome/compara/index.html#species_tree">here</a> on how it is constructed).
-Click the icons on the blue image bar below to interact with the tree or download the
-<a href="species_tree.pdf" id="speciestree">Static image</a> in PDF.
-You can download the data in Newick format from our GitHub repository:
 </p>
 <ul>
 <li>Topology Only: <a href="https://github.com/Ensembl/ensembl-compara/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/scripts/pipeline/species_tree.ensembl.topology.nw">all species</a></li>

diff --git a/widgets/htdocs/widgets/95_SpeciesTree.js b/widgets/htdocs/widgets/95_SpeciesTree.js
@@ -131,15 +131,22 @@ Ensembl.SpeciesTree.tnt_theme_tree_simple_species_tree = function(species_detail
             pdf.text(0.5, 0.5, tree_label || '');
             pdf.save(filename);
           }
-          else {
-            var download = document.getElementById('download');
+          else if(exportType == 'PNG') {
             var a = document.createElement("a");
             a.download = filename;
             a.href = imgsrc;
             document.body.appendChild(a);
             a.click();
             $(a).remove();          
           }
+          else {
+            var tree_type = d3.select(".tree_menu").select(".current").attr("class").replace(/current/g,'').replace(/tree_item/g,'').replace(/ /g,'');
+            var newick = species_details['trees'][tree_type].newick;
+            var a = document.createElement("a");
+            a.download = filename;
+            a.href="data:text/plain,"+encodeURIComponent(newick);
+            a.click();
+          }
           element && $(element).html(exportType);
           element && $(element).removeClass('loading');
         };
@@ -324,13 +331,16 @@ Ensembl.SpeciesTree.tnt_theme_tree_simple_species_tree = function(species_detail
           .attr("class", "header")
           .text("Choose download type");
 
+
+      $.each(['Newick', 'PNG'], function(i, type) {
         export_menu.append("div")
-          .attr("class", "Export_PNG")
-          .text('PNG')
+          .attr("class", "Export_" + type)
+          .text(type)
           .on("click", function(){
             var svgElement = $($('.js_tree'));
-            svgExport(svgElement[0], 'PNG', this);
+            svgExport(svgElement[0], type, this);
            });
+      });
 
       $.when(_jspdf).done(function() {
         export_menu.append("div")
@@ -342,7 +352,6 @@ Ensembl.SpeciesTree.tnt_theme_tree_simple_species_tree = function(species_detail
           });
       })
 
-
       var export_icon = d3.select(".image_toolbar")
           .append("div")
           .attr("class", "export")

diff --git a/widgets/modules/EnsEMBL/Web/Document/HTML/Compara/SpeciesTree.pm b/widgets/modules/EnsEMBL/Web/Document/HTML/Compara/SpeciesTree.pm
@@ -105,8 +105,7 @@ sub render {
 
      if ($sp->{production_name}) {
         my $sp_icon = $species_defs->ENSEMBL_WEBROOT . '/../public-plugins/ensembl/htdocs/i/species/48/' . $sp->{production_name} . '.png';
-        my $check = file_exists($sp_icon);
-        if (!$check->{'error'}) {
+        if (file_exists($sp_icon)) {
           my $content = read_file($sp_icon);
           if ($content) {
             $sp->{icon} = 'data:image/png;base64,'.encode_base64($content);