rbbt-views 1.0.0 → 1.0.1

data/share/views/edit_list.haml

@@ -0,0 +1,39 @@
+%a(href="/entity_list/#{ type }/#{ id }") View
+
+%form(action="#{File.join('/entity_list', type, 'copy', id)}" method='post')
+  %label Copy as:
+  %input(name='new_id')
+  %input(type='submit')
+
+%form(action="#{File.join('/entity_list', type, 'add', id)}" method='post')
+  %label Add other list:
+  %select.loaded_lists(name="other_list" type=type)
+  %input(type='submit')
+
+%form(action="#{File.join('/entity_list', type, 'subset', id)}" method='post')
+  %label Subset other list:
+  %select.loaded_lists(name="other_list" type=type)
+  %input(type='submit')
+
+%form(action="#{File.join('/entity_list', type, 'remove', id)}" method='post')
+  %label Remove other list:
+  %select.loaded_lists(name="other_list" type=type)
+  %input(type='submit')
+
+
+%ul.entity_list
+  - list.each do |entity|
+    - values = {}
+    - types = {}
+    - entity.info.each{|k,v| values[k] = String === v ? v : v.to_json; types[k] = :string }
+
+    %li(id="#{entity.id}")
+      = entity.respond_to?(:link) ? entity.link : entity
+      \.
+      %a.DELETE.remove_entity_from_list(rel="#{entity.id}" href="/entity_list/#{ type }/#{ entity }/#{ id }") remove
+      -#- form_id = "edit_entity_#{id}_#{entity.to_s}".gsub(/\s/, '_')
+      -#%a.open_edit_controls(href="#edit_controls" ref=form_id) edit
+      -#.edit_controls
+      -#  - action = File.join("/entity_list", type, entity, id)
+      -#  = workflow_partial('partials/_form', workflow, :values => values, :inputs => values.keys, :input_types => types, :action => action, :method => "post", :id => form_id)
+

data/share/views/entity/GenomicMutation.haml

@@ -3,8 +3,18 @@
 %p== reference base: #{entity.reference}
 %p== Genes: #{entity.genes.nil? ? "none" : entity.genes.link * ", "}
 
+- if entity.in_exon_junction?
+  %p In Exon Junction
+
 %a(href="#{entity.ensembl_browser}") Ensembl Browser
 
 %ul
   - (entity.mutated_isoforms || []).select{|mi| mi.consequence != "SYNONYMOUS"}.each do |mi|
-    %li= mi.link
+    %li
+      = mi.link
+      %span.note
+        - pdbs = mi.pdbs
+        - if pdbs.nil? or pdbs.empty?
+          [No PDBs]
+        - else 
+          == [#{pdbs.length} PDBs]

data/share/views/entity/KeggPathway.haml

@@ -1,12 +1,14 @@
 %h3= entity.name
 
-- genes_in_pathway = Gene.setup(KEGG.index2genes[entity], "KEGG Gene ID", "Hsa").from_kegg
+- genes_in_pathway = Gene.setup(KEGG.index2genes[entity], "KEGG Gene ID", entity.organism).from_kegg
 
 %dl
   %dt Description
   %dd= entity.description
 
-  %dt All Genes in pathway
+  %dt 
+    All Genes in pathway
+    == (#{ genes_in_pathway.ensembl.list_link :length, "Genes in pathway #{entity.name}"})
   %dd= genes_in_pathway.from_kegg.link * ", "
 
 %img(src='http://www.genome.jp/kegg/pathway/hsa/#{entity}.png' style='width:100%;float:left;margin-right:10px;margin-botton:10px;' title='Click to see KEGG entry')

data/share/views/entity/MutatedIsoform.haml

@@ -1,8 +1,5 @@
 %h1= entity
-= entity.transcript.gene.link
-
-.svg(style="width:100%")
-  = entity.marked_svg
+= entity.action_link 'marked_svg', "Protein overview", :link_options => {:extra_classes => "replace"}
 
 %dl
   %dt MutationAssesor prediction
@@ -12,32 +9,7 @@
   %dd= entity.damage_scores([:sift])
 
 
- 
-- pdbs = entity.pdbs
-- if pdbs and pdbs.any?
-  #jmol
-    %hr
-    %select.pdb
-      %option(selected="selected") Select a pdb
-      - pdbs.each do |pdb, info| 
-        - pdb_chain = info[:chains].split("/").first
-        - pdb_position = entity.position - info[:region].begin + 1
-        %option(attr-chain=pdb_chain attr-position=pdb_position attr-pdb=pdb)= "#{ pdb} (#{[pdb_position, pdb_chain] * "/"})"
-    
-    #jmol_image
-
-    :javascript
-
-      jmolSetXHTML('jmol_image')
-
-      jmolApplet(500, "", "PIZARRA");
-      $('select.pdb').change(function(){
-        var option = $(this).find('option:selected');
-        var pdb = option.attr('attr-pdb');
-        if (pdb == "Select a pdb") return false
-        var pdb_position = option.attr('attr-position');
-        var pdb_chain = option.attr('attr-chain');
-        jmolScript("load =" + pdb + "; wireframe off; restrict water; select protein; backbone off; color pink;cartoons on;color structure; select protein and *.CA and " + pdb_position + ":" + pdb_chain + "; spacefill; color blue;", "PIZARRA");
-      })
-
-
+- if entity.pdbs and entity.pdbs.any?
+  = entity.action_link 'pdbs', "Mutation over pdbs", :link_options => {:extra_classes => "replace"}
+- else
+  No pdbs found

data/share/views/entity/MutatedIsoform/marked_svg.haml

@@ -0,0 +1,3 @@
+.svg(style="width:100%")
+  = entity.marked_svg || "Could not download protein SVG"
+

data/share/views/entity/MutatedIsoform/pdbs.haml

@@ -0,0 +1,33 @@
+- pdbs = entity.pdbs_and_positions
+- if pdbs and pdbs.any?
+  #jmol
+    %select.pdb
+      %option(selected="selected") Select a pdb
+      - found = 0
+      - pdbs.each do |pdb, chains| 
+        - chains.each do |pdb_chain, pdb_position|
+          - next if pdb_position.nil?
+          - pdb_position -= 1
+          %option(attr-chain=pdb_chain attr-position=pdb_position attr-pdb=pdb)= "#{ pdb} (#{[pdb_position, pdb_chain] * "/"})"
+          - found += 1
+    
+    - if found == 0
+      No pdbs cover that position
+    - else
+      #jmol_image
+
+      :javascript
+
+        jmolSetXHTML('jmol_image')
+
+        jmolApplet(500, "", "PIZARRA");
+        $('select.pdb').change(function(){
+          var option = $(this).find('option:selected');
+          var pdb = option.attr('attr-pdb');
+          if (pdb == "Select a pdb") return false
+          var pdb_position = option.attr('attr-position');
+          var pdb_chain = option.attr('attr-chain');
+          jmolScript("load =" + pdb + "; wireframe off; restrict water; select protein; backbone off; color pink;cartoons on;color structure; select protein and *.CA and " + pdb_position + ":" + pdb_chain + "; spacefill; color blue;", "PIZARRA");
+        })
+
+

data/share/views/entity/NCIBioCartaPathway.haml

@@ -0,0 +1,11 @@
+%h3= entity.name
+
+- genes_in_pathway = entity.genes.ensembl
+
+%dl
+
+  %dt 
+    All Genes in pathway
+    == (#{ genes_in_pathway.ensembl.list_link :length, "Genes in pathway #{entity.name}"})
+  %dd= genes_in_pathway.link * ", "
+

data/share/views/entity/NCINaturePathway.haml

@@ -0,0 +1,11 @@
+%h3= entity.name
+
+- genes_in_pathway = entity.genes.ensembl
+
+%dl
+
+  %dt 
+    All Genes in pathway
+    == (#{ genes_in_pathway.ensembl.list_link :length, "Genes in pathway #{entity.name}"})
+  %dd= genes_in_pathway.link * ", "
+

data/share/views/entity/NCIReactomePathway.haml

@@ -0,0 +1,11 @@
+%h3= entity.name
+
+- genes_in_pathway = entity.genes.ensembl
+
+%dl
+
+  %dt 
+    All Genes in pathway
+    == (#{ genes_in_pathway.ensembl.list_link :length, "Genes in pathway #{entity.name}"})
+  %dd= genes_in_pathway.link * ", "
+

data/share/views/entity/Protein.haml

@@ -0,0 +1,5 @@
+%header== Protein: #{entity}
+
+%dl
+  %dt Gene
+  %dd= entity.gene.link

data/share/views/entity_list/Default.haml

@@ -1,10 +1 @@
-%ul.entity_list
-  - list.each do |elem|
-    %li
-      - case
-      - when elem.respond_to?(:link)
-        = elem.link
-      - when elem.respond_to?(:name)
-        = elem.name
-      - else
-        = elem
+= (list.respond_to?(:link)? list.link : list) * ", "

data/share/views/js/app.js

@@ -60,7 +60,8 @@ function expand_details(){
   var url =  $('#details').attr('url');
   if (url == null) return false;
 
-  $.ajax(add_parameters(url, '_size=normal'), {
+  $.ajax(add_parameters(url, '_size=normal&_cache_type=memory'), {
+    cache: false,
     success: function(data){
       $('#details').html(data).attr('url', url);
       $('#main').hide()
@@ -80,7 +81,8 @@ function contract_details(){
   var url =  $('#details').attr('url');
   if (url == null) return false;
  
-  $.ajax(add_parameters(url, '_size=small'), {
+  $.ajax(add_parameters(url, '_size=small&_cache_type=memory'), {
+    cache: false,
     success: function(data){
       $('#details').html(data).attr('url', url);
       $('#main').show()
@@ -106,7 +108,8 @@ function back_details(){
       size = "small";
     }
  
-    $.ajax(add_parameters(url, '_size=' + size), {
+    $.ajax(add_parameters(url, '_size=' + size + "&_cache_type=memory"), {
+      cache: false,
       success: function(data){
         $('#details').html(data).attr('url', url);
         rbbt_action_setup();
@@ -121,31 +124,216 @@ function back_details(){
 
 // REPLACE OBJECTS
 
-function replace_object(obj){
+function replace_object(obj, update){
   var href = obj.attr('href');
 
+
   if (href == null || href == undefined || href == ""){href = obj.attr('target');}
   if (href == null || href == undefined || href == ""){href = obj.attr('url');}
 
+  if (update == 'reload'){
+    href = add_parameters(href, "_update=reload")
+  }
+
+  if (update == 'check'){
+    href = add_parameters(href, "_update=check")
+  }
+
   $.ajax(href,{
+    cache: false,
     beforeSend: function(){obj.addClass("reloading")},
     complete: function(){obj.removeClass("reloading")},
+    error: function( req, text, error ) {
+      obj.removeClass("reloading");
+      obj.addClass("error");
+      if (obj.find('span[class*=cache_status]').length == 0){
+        obj.html(obj.html() + "<span class='cache_status'>error</status>").after($("<a class='retry_error'>retry</a>"))
+      }else{
+        obj.after($("<a class='retry_error'>retry</a>")).find('span[class*=cache_status]').first().html("error") 
+      }
+      rbbt_action_setup();
+    },
     success: function( data, stat, req ) {
-      var html = '<div class="embedded" target="' + req.getResponseHeader("AJAX-URL")  + '">' + data + '</div>';
-      var embedded = $(html);
-      embedded.addClass(obj.attr('class'));
-      embedded.removeClass('replace');
-      embedded.removeClass('rbbt_action_setup');
-      obj.replaceWith(embedded);
       if (req.status == 202){
-        embedded.addClass("reloading");
-        window.setTimeout(function(){replace_object(embedded)}, 5000)
+        obj.addClass("reloading");
+
+        if (obj.find('span[class*=cache_status]').length == 0){
+          obj.html(obj.html() + data)
+        }else{
+          obj.find('span[class*=cache_status]').first().replaceWith($(data))
+        }
+
+        if (update == 'check'){
+          obj.removeClass("reloading");
+          obj.addClass("check");
+          if (obj.find('span[class*=cache_status]').length == 0){
+            obj.after($("<a class='start_checked'>start</a>"));
+          }else{
+            obj.after($("<a class='start_checked'>start</a>"));
+          }
+          rbbt_action_setup();
+        }else{
+          window.setTimeout(function(){replace_object(obj)}, 7000)
+        }
       }else{
+        var html = '<div class="embedded" target="' + req.getResponseHeader("AJAX-URL")  + '">' + data + '</div>';
+        var embedded = $(html);
+        embedded.addClass(obj.attr('class'));
+        embedded.removeClass('replace');
+        embedded.removeClass('rbbt_action_setup');
         embedded.removeClass("reloading");
+        obj.replaceWith(embedded);
         rbbt_action_setup();
       }
+ 
+    },
+   });
+}
+
+function expand_embedded(embedded){
+  var header = embedded.find('header').first();
+  embedded.html(embedded.attr('attr-save'));
+  embedded.attr('attr-save',null);
+  embedded.removeClass('contracted_embedded');
+  embedded.removeClass('rbbt_action_setup').find('.rbbt_action_setup').removeClass('rbbt_action_setup');
+  rbbt_action_setup();
+}
+
+function contract_embedded(embedded){
+  var header = embedded.find('header').first();
+  embedded.attr('attr-save', embedded.html());
+  embedded.html(header.html());
+  embedded.addClass('contracted_embedded');
+  embedded.removeClass('rbbt_action_setup').find('.rbbt_action_setup').removeClass('rbbt_action_setup');
+  rbbt_action_setup();
+}
+
+//-- LIST MANAGEMENT
+
+var entity_lists = {}
+
+function saved_lists(){
+  return JSON.parse($.cookie('saved_lists'))
+}
+
+function remove_list(type, list){
+  var lists = saved_lists();
+  if (lists == null) { lists = {}; };
+  if (lists[type] == null) { lists[type] = [] };
+
+  var elems = lists[type]
+  if (elems != null){
+    var index = elems.indexOf(list);
+
+    if (index != -1){ elems.splice(index, 1);}
+
+    if (elems.length > 0){
+      lists[type] = elems;
+    }else{
+      delete lists[type]
+    }
+
+    delete entity_lists[type][list]
+    if (entity_lists[type].length == 0){
+      delete entity_lists[type]
     }
-    });
+  }
+
+  $.cookie('saved_lists', JSON.stringify(lists), {path: "/"})
+
+  update_list_viewer()
+}
+
+function load_list(type, list){
+  var lists = saved_lists();
+  if (lists == null) { lists = {}; };
+  if (lists[type] == null) { lists[type] = [] };
+  lists[type].push(list);
+  $.cookie('saved_lists', JSON.stringify(lists), {path: "/"})
+  add_entity_list(type, list);
+}
+
+function record_list(type, list_id, list){
+  if (entity_lists[type] == null){
+    entity_lists[type] = {}
+  }
+  entity_lists[type][list_id] = list;
+}
+
+function update_list_viewer(){
+  var list_html = ""
+  list_html += "<a href='/entity_list/user'>your lists</a>\n"
+  list_html += "<a href='/entity_list/public'>public lists</a>\n"
+  list_html += "<a class='clear_selected' href='#clear_selected'>clear selected</a>\n"
+  list_html += "<h5 class='loaded_lists'>Loaded lists</h5>\n"
+  list_html += "<dl class='entity_list_types'>\n"
+  $.each(entity_lists, function(type, lists){
+    list_html += "<dt>" + type + "</dt>\n"
+    list_html += "<dd>\n"
+    list_html += "<ul class='entity_list'>"
+    $.each(lists, function(name, elems){
+      list_html += "<li>"
+
+      list_html += "<a href='#select_list' class='select_list' attr-list-type='" + type + "' attr-list='" + name + "'>"
+      list_html += 'select'
+      list_html += "</a>" + "\n"
+
+      list_html += "<a href='#remove_list' class='remove_list' attr-list-type='" + type + "' attr-list='" + name + "'>"
+      list_html += "remove"
+      list_html += "</a>" + "\n"
+
+      list_html += "<a href='/entity_list/" + type + "/" + name + "' class='view_list' attr-list-type='" + type + "'>"
+      list_html += name
+      list_html += "</a>" + "\n"
+
+      list_html += "</li>"
+    })
+    list_html += "</ul>"
+    list_html += "</dd>\n"
+  })
+  $('#lists').html(list_html);
+  rbbt_action_setup();
+}
+
+function update_list_selectors(){
+  $.each(entity_lists, function(type, lists){
+    $('select.loaded_lists[type=' + type + ']').each(function(){
+      var select = $(this);
+      select.find('option').remove();
+      $.each(lists, function(name, elems){
+        var option = $('<option value="' + name + '">' + name + '</option>')
+        select.append(option);
+        return true
+      })
+    })
+  });
+}
+
+function add_entity_list(type, list_id){
+  $.getJSON(
+    "/entity_list/" + type + "/" + list_id + '?_format=json',
+  function(data){ 
+    record_list(type, list_id, data); 
+    update_list_viewer();
+    update_list_selectors();
+  })
+}
+
+function id_for_entity(entity_format, entity){
+  return((entity_format.toLowerCase().replace(/[^\w]/g, "_") + "=" + entity));
+}
+
+function select_list(type, list_id){
+  var list = entity_lists[type][list_id];
+  var entity;
+
+  $.each(list, function(id, data){
+    var id =  data[0];
+    var info = data[1];
+    var format = info["format"];
+    var entity_id = id_for_entity(format, id);
+    $('.entity[' + entity_id + ']').addClass("selected_entity");
+  })
 }
 
 //-- SETUP FUNCTIOS
@@ -163,6 +351,7 @@ function rbbt_table_setup(){
         var psize =  form.find(".psize").first().val();
         var change = $(this).val();
         $.ajax({
+          cache: false,
           url: add_parameters(href, "_pfield=" + pfield + "&_pnum=" + pnum + "&_psize=" + psize + "&_paginate=" + change),
           success: function(data){
             embedded_div.html(data);
@@ -197,6 +386,11 @@ function rbbt_action_setup(){
     replace_object($(this));
   }).addClass('rbbt_action_setup');
 
+  $('a.check_replace').not('[class*=rbbt_action_setup]').each(function(){
+    replace_object($(this), 'check');
+  }).addClass('rbbt_action_setup');
+
+
   $('a.entity').not('[class*=rbbt_action_setup]').click(function(){
     var link = $(this);
     var href = link.attr('href')
@@ -210,7 +404,8 @@ function rbbt_action_setup(){
     show_details();
     $('#details').html("<span class='details_loading'>Loading " + href + "</span>").addClass("loading").removeClass("error");
 
-    $.ajax(add_parameters(href, '_size=' + size), {
+    $.ajax(add_parameters(href, '_size=' + size + '&_cache_type=memory'), {
+      cache: false,
       success: function(data){
         var old_url = $('#details').attr('url');
         if (old_url != null && old_url != undefined ){
@@ -230,46 +425,148 @@ function rbbt_action_setup(){
   }).addClass('rbbt_action_setup');
 
   $('.DELETE,.POST').not('[class*=rbbt_action_setup]').click(function() {
-    if(confirm('Are you sure?')) {
+    //if(confirm('Are you sure?')) {
+    if(true) {
       var link = $(this);
-      var href = link.attr('href')
+      var target_id = link.attr('rel')
+      var href = link.attr('href');
 
-      $.ajax({url:href, data:{ _method: $(this).getClassInList(['POST', 'DELETE'])}, type:"post", asyn:false})
+      $.ajax({cache: false, url:href, data:{ _method: $(this).getClassInList(['POST', 'DELETE'])}, type:"post", asyn:false, success: function(){if (target_id != null){ link.remove(); $("#" + target_id).remove();}}})
     }
     return false;
   }).addClass('rbbt_action_setup');
 
-  //$('form.replace').not('[class*=rbbt_action_setup]').each(function(){
-  //  var link = $(this);
-  //  var href = link.attr('href')
-  //  $.ajax(href,{
-  //    success: function( data, stat, req ) {
-  //      link.replaceWith('<div class="embedded" target="' + req.getResponseHeader("AJAX-URL")  + '">' + data + '</div>');
-  //      rbbt_action_setup();
-  //    }
-  //  });
-  //}).addClass('rbbt_action_setup');
-
   $('div.embedded form').not('[class*=rbbt_action_setup]').submit(function(){
     var form = $(this);
     var embedded = form.parents('div.embedded').first();
 
-    form.ajaxSubmit({
-      success: function( data, stat, req){
-        embedded.html(data);
-        rbbt_action_setup();
-      },
-      beforeSend: function(){
-        embedded.addClass("reloading");
-      },
-      complete: function(){
-        embedded.removeClass("reloading");
+    var params = "";
+
+    form.find('input').not('[type=submit]').each(function(){
+      var input = $(this)
+      if (params.length > 0){ params += '&'}
+      params += input.attr('name') + "=" + input.val();
+    })
+
+    form.find('select').not('[type=submit]').each(function(){
+      var select = $(this)
+      var option = select.find('option:selected');
+      if (params.length > 0){ params += '&'}
+      params += select.attr('name') + "=" + option.val();
+    })
+
+
+    params = params
+
+    var url = embedded.attr('target');
+    url = url.replace(/\?.*/, '?' + params) 
+
+    embedded.attr('target', url)
+
+    replace_object(embedded);
+
+    return false;
+  }).addClass('rbbt_action_setup');
+
+  $('.embedded > header').not('[class*=rbbt_action_setup]').each(function(){
+    var header = $(this);
+    var embedded = header.parent('.embedded');
+    var href = embedded.attr('target');
+
+    if (header.find('ul.embedded_control').length == 0){
+      var html = header.html();  
+      html = html + '<ul class="embedded_control"><li><a class="toggle_embedded">toggle</a></li><li><a class="reload_embedded">reload</a></li><li><a class="link_embedded" href="'+ href + '">link</a></li></ul>'
+      header.html(html);
+    }
+
+    header.addClass('rbbt_action_setup')
+
+    rbbt_action_setup();
+  }).addClass('rbbt_action_setup');
+
+  $('a.reload_embedded').not('[class*=rbbt_action_setup]').click(function(){
+    var link = $(this);
+    var embedded = link.parents('.embedded').first();
+    if (embedded.hasClass('contracted_embedded')){
+      expand_embedded(embedded)
+    }
+    replace_object(embedded, 'reload');
+    return false;
+  }).addClass('rbbt_action_setup');
+
+  $('a.toggle_embedded').not('[class*=rbbt_action_setup]').click(function(){
+    var link = $(this);
+    var embedded = link.parents('.embedded').first();
+    var header = embedded.find('header').first();
+
+    if (embedded.attr('attr-save') == null){
+      contract_embedded(embedded)    
+      }else{
+        expand_embedded(embedded)    
       }
-    });
+      return false;
+    }).addClass('rbbt_action_setup');
+
+    $('a.retry_error').not('[class*=rbbt_action_setup]').click(function(e){
+      var retry_link = $(this);
+      var link = retry_link.prev('a');
+      if (link.length == 0){ link = retry_link.prev('.embedded')};
+      replace_object(link, 'reload');
+      retry_link.remove();
+      return false;
+    }).addClass('rbbt_action_setup');
+
+
+    $('a.start_checked').not('[class*=rbbt_action_setup]').click(function(e){
+      var retry_link = $(this);
+      var link = retry_link.prev('a');
+      replace_object(link);
+      retry_link.remove();
+      return false;
+    }).addClass('rbbt_action_setup');
+
+    $('a.select_list').not('[class*=rbbt_action_setup]').click(function(){
+      var link = $(this);
+      var list_id = link.attr('attr-list')
+      var type = link.attr('attr-list-type')
+
+      select_list(type, list_id)
+      return false;
+    }).addClass('rbbt_action_setup');
 
+    $('a.remove_list').not('[class*=rbbt_action_setup]').click(function(){
+      var link = $(this);
+      var list_id = link.attr('attr-list');
+      var type = link.attr('attr-list-type')
+
+      remove_list(type, list_id);
+
+      return false;
+    }).addClass('rbbt_action_setup');
+
+
+    $('a.load_entity_list').not('[class*=rbbt_action_setup]').click(function(){
+      var link = $(this);
+    var list_id = link.attr('attr-list');
+    var type = link.attr('attr-list-type');
+
+    load_list(type, list_id);
     return false;
   }).addClass('rbbt_action_setup');
 
+  $('a.open_edit_controls').not('[class*=rbbt_action_setup]').click(function(){
+    var link = $(this);
+
+    var edit_controls = link.next('.edit_controls')
+    edit_controls.toggle();
+
+    return false;
+  }).addClass('rbbt_action_setup');
+
+  $('a.clear_selected').not('[class*=rbbt_action_setup]').click(function(){
+    $('a.selected_entity').removeClass('selected_entity')
+  }).addClass('rbbt_action_setup');
 
+  update_list_selectors();
 }