rbbt-views 1.0.1 → 2.0.0

data/share/views/entity/NCIBioCartaPathway.haml

@@ -1,11 +1,10 @@
 %h3= entity.name
 
-- genes_in_pathway = entity.genes.ensembl
+- genes_in_pathway = Gene.setup(entity.genes.ensembl, "Ensembl Gene ID", entity.organism)
 
 %dl
-
   %dt 
     All Genes in pathway
-    == (#{ genes_in_pathway.ensembl.list_link :length, "Genes in pathway #{entity.name}"})
+    == (#{ genes_in_pathway.list_link :length, "Genes in pathway #{entity.name}"})
   %dd= genes_in_pathway.link * ", "
 

data/share/views/entity/NCINaturePathway.haml

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

data/share/views/entity/NCIReactomePathway.haml

@@ -1,11 +1,10 @@
 %h3= entity.name
 
-- genes_in_pathway = entity.genes.ensembl
+- genes_in_pathway = Gene.setup(entity.genes.ensembl, "Ensembl Gene ID", entity.organism)
 
 %dl
-
   %dt 
     All Genes in pathway
-    == (#{ genes_in_pathway.ensembl.list_link :length, "Genes in pathway #{entity.name}"})
+    == (#{ genes_in_pathway.list_link :length, "Genes in pathway #{entity.name}"})
   %dd= genes_in_pathway.link * ", "
 

data/share/views/entity/PfamDomain.haml

@@ -1 +1,3 @@
 %h3= entity.name
+
+%a(href="http://pfam.sanger.ac.uk/family/#{entity}") PFAM

data/share/views/entity/Transcript.haml

@@ -0,0 +1,10 @@
+%h3= entity
+
+%dl
+  %dt Exons
+  %dd= entity.exons.sort * ", "
+
+%p
+  %a(href="http://jun2011.archive.ensembl.org/Homo_sapiens/Transcript/Summary?t=#{entity}")= entity
+
+%img(src="#{entity.protein.ensembl_protein_image_url}")

data/share/views/entity_list/Default.haml

@@ -1 +1,5 @@
+= workflow_partial('partials/_list_header', :id => id, :entity_type => entity_type, :format => format)
+
+%p== #{list.length} elements
+
 = (list.respond_to?(:link)? list.link : list) * ", "

data/share/views/entity_list/Default/compare_to_other_lists.haml

@@ -0,0 +1,41 @@
+- other_list ||= nil
+
+- if other_list and not other_list.empty?
+  %header== Compare list #{ id } with list #{other_list}
+- else
+  %header== Compare list #{ id } with other lists
+
+%form(action="#{File.join('/entity_list_action', entity_type, 'compare_to_other_lists', id)}" method='post')
+  %label Compare to:
+  %select.loaded_lists(name="other_list" type=entity_type)
+  %input(type='submit')
+
+- if  not other_list.nil? and not other_list.empty?
+  - other = Entity::REST.load_list(entity_type, other_list, user)
+  - exclusive = list.remove other
+  - common = list.subset other
+  - union = list.annotate(list + other).uniq
+  %dl
+    %dt Exclusive
+    %dd
+      - if exclusive.any?
+        = exclusive.list_link :length, "(#{ id } - #{ other_list })"
+      - else
+        None
+
+    %dt Common
+    %dd
+      - if common.any?
+        = common.list_link :length, "(#{ id } AND #{ other_list })"
+      - else
+        None
+
+    %dt Union
+    %dd
+      - if union.any?
+        = union.list_link :length, "(#{ id } + #{ other_list })"
+      - else
+        None
+
+
+

data/share/views/entity_list/Default/entity_links.haml

@@ -0,0 +1,6 @@
+%header== Entities in list #{ id }
+- list = list.name.compact.sort if list.respond_to?(:name) and defined? sort and sort
+- list = list.ensembl if list.respond_to? :ensembl
+
+= (list.respond_to?(:link) ? list.link : list) * ", "
+

data/share/views/entity_list/Default/find_in_other_lists.haml

@@ -0,0 +1,36 @@
+- lists ||= nil
+
+%header.find_genes_in_other_lists Find genes in other loaded lists
+
+- if lists.nil? 
+  :javascript
+    var entity_type = '#{entity_type}';
+    var lists = saved_lists()[entity_type];
+    var url = '#{File.join('/entity_list_action', entity_type, 'find_in_other_lists', id)}' + "?lists=" + lists.join("|");
+    var header = $('header.find_genes_in_other_lists')
+
+    if ( header.parent('.embedded').length != 0){
+      var embedded = header.parent('.embedded').first();
+      embedded.attr('href', url);
+      $('header.find_genes_in_other_lists').after('<a class="find_genes_in_other_lists" href="' + url + '">Compare with ' + lists.length + ' lists</a>')
+      $('a.find_genes_in_other_lists').click(function(){
+        replace_object(embedded, false);
+        return false;
+      })
+    }else{
+      window.location = url
+    }
+
+- else
+  %dl
+  - lists.split("|").each do |list_name|
+    - other_list = Entity::REST.load_list(entity_type, list_name, user).subset(list)
+    %dt 
+      Subset of
+      = other_list.list_link :length, "Common between #{id} and #{list_name}"
+      common elements with list
+      %a(href="http://cotos:1900/entity_list/#{ entity_type }/#{ list_name }")=list_name
+    %dd
+      = other_list.link * ", "
+      
+

data/share/views/error.haml

@@ -1,2 +1,7 @@
-%span.error=step.messages.last
+%header.error Error
+%span.error= escape_html message
+- if defined? backtrace and backtrace
+  %ul.backtrace
+    - backtrace.each do |line|
+      %li.message= escape_html line
 

data/share/views/find.haml

@@ -0,0 +1,10 @@
+
+%form.find(method='POST' action='/find')
+  %label Find
+  %input#find(type='text' name='term')
+  #find_wrapper
+
+%style
+  :sass
+:javascript
+  

data/share/views/form.haml

@@ -11,4 +11,4 @@
     %h3 Other jobs
     %a.replace(href="/#{File.join(workflow.to_s, task, 'jobs')}") jobs
 
-= workflow_partial('partials/_form', :inputs => inputs, :input_types => input_types, :input_defaults => input_defaults, :input_descriptions => input_descriptions, :values => params, :id => id, :jobname => export != :exec, :email => export == :asynchronous, :klass => 'task' )
+= workflow_partial('partials/_form', :inputs => inputs, :input_options => input_options, :input_types => input_types, :input_defaults => input_defaults, :input_descriptions => input_descriptions, :values => params, :id => id, :jobname => export != :exec, :email => export == :asynchronous, :klass => 'task' )

data/share/views/info.haml

@@ -1,4 +1,4 @@
-%dl
+%dl.info
   - info.each do |key, value|
     %dt= key
     %dd

data/share/views/js/_action_setup.js

@@ -0,0 +1,250 @@
+function rbbt_action_setup(){
+  rbbt_table_setup();
+
+  $('a.replace, a.check_replace').not('[class*=rbbt_action_setup]').each(function(){
+    var link = $(this);
+    if ($.inArray(unescape(link.attr('href')), closed_sections) != -1){
+      // I don't know what these clases are repeated and I have to remove them
+      // twice
+      link.removeClass('replace');
+      link.removeClass('replace');
+      link.removeClass('check_replace');
+      link.removeClass('check_replace');
+      link.addClass('closed_replace');
+      link.addClass('closed_replace');
+    }
+  });
+
+  $('a.replace').not('[class*=rbbt_action_setup]').each(function(){
+    replace_object($(this));
+  }).addClass('rbbt_action_setup');
+
+  $('a.check_replace').not('[class*=rbbt_action_setup]').each(function(){
+    replace_object($(this), 'check');
+  }).addClass('rbbt_action_setup');
+
+  $('a.closed_replace').not('[class*=rbbt_action_setup]').each(function(){
+    var obj = $(this);
+    if (obj.find('span[class*=status]').length == 0){
+      obj.after($("<a class='start_checked'>open</a>"));
+    }else{
+      obj.after($("<a class='start_checked'>open</a>"));
+    }
+  }).addClass('rbbt_action_setup');
+
+
+  $('div.toggle').each(function(){
+    var toggle = $(this);
+    var content = toggle.html();
+    var title_text = toggle.attr('title');
+
+    var title = "<dt>" + title_text + "</dt>";
+    var description = "<dd>" + content + "</dd>";
+    var dl = $("<dl class='toggle'>" + title + description + "</dl>");
+
+    toggle.replaceWith(dl);
+    dl.find('title').click(function(){
+      var dt = $(this)
+      var dl = dt.parent('dl');
+      var dd = dl.find('>dd').first();
+      dd.toggle();
+      if (dd.visible()){
+        dt.addClass('opened');
+      }else{
+        dt.removeClass('opened');
+      }
+      rbbt_action_setup();
+    });
+    dl.find('title > dd').hide();
+  })
+
+  $('dl.toggle > dt').not('[class*=rbbt_action_setup]').click(function(){
+    var dl = $(this).parent('dl');
+    var dd = dl.find('>dd');
+    var dt = dl.find('>dt');
+
+    dd.toggle();
+
+    if (dd.is(':visible')){
+      dt.addClass('opened');
+    }else{
+      dt.removeClass('opened');
+    }
+
+    rbbt_action_setup();
+
+  }).addClass('rbbt_action_setup');
+
+  $('dl.toggle > dd').not('[class*=rbbt_action_setup]').each(function(){
+    $(this).hide();
+  }).addClass('rbbt_action_setup');
+
+  $('div.embedded form').not('[class*=rbbt_action_setup]').submit(function(){
+    var form = $(this);
+    var embedded = form.parents('div.embedded').first();
+
+    var params = "";
+
+    form.find('input').not('[type=submit]').not('[type=radio]').each(function(){
+      var input = $(this)
+      if (params.length > 0){ params += '&'}
+      params += input.attr('name') + "=" + input.val();
+    })
+
+    form.find('input[type=radio]:checked').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();
+    })
+
+    form.find('textarea').each(function(){
+      var input = $(this)
+      if (params.length > 0){ params += '&'}
+      params += input.attr('name') + "=" + escape(input.val());
+    })
+
+    params = params
+    
+    var url = embedded.attr('target');
+
+    if (url.indexOf('?') == -1){
+      url = url + '?' + params;
+    }else{
+      url = url.replace(/\?.*/, '?' + params);
+    }
+
+    embedded.attr('target', url)
+
+    replace_object(embedded);
+
+    return false;
+  }).addClass('rbbt_action_setup');
+
+  $('a.delete_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, 'delete');
+    return false;
+  }).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.abort_embedded').not('[class*=rbbt_action_setup]').click(function(e){
+    var abort_link = $(this);
+    var link = abort_link.prev('a');
+    if (link.length == 0){ link = abort_link.prev('.embedded')};
+    replace_object(link, 'abort');
+    abort_link.remove();
+    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 start_link = $(this);
+    var link = start_link.prev('a');
+    replace_object(link);
+    start_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');
+    select_cytoscape([]);
+    return false;
+  }).addClass('rbbt_action_setup');
+
+  $('a.update_list_viewer').not('[class*=rbbt_action_setup]').click(function(){
+    update_saved_lists()
+    return false;
+  }).addClass('rbbt_action_setup');
+
+
+  update_list_selectors();
+
+  zoomable_images($('#main'));
+  zoomable_images($('#details'));
+
+  update_dom()
+}
+
+

data/share/views/js/_basic.js

@@ -0,0 +1,269 @@
+if(!Array.indexOf){
+  Array.prototype.indexOf = function(obj){
+    for(var i=0; i<this.length; i++){
+      if(this[i]==obj){
+        return i;
+      }
+    }
+    return -1;
+  }
+}
+
+Array.prototype.remove = function(elem) {
+  var match = -1;
+
+  while( (match = this.indexOf(elem)) > -1 ) {
+    this.splice(match, 1);
+  }
+};
+
+Array.prototype.uniq = function() {
+ var myarray = this;
+
+ new_arr = myarray.filter(function(elem, pos) {
+      return myarray.indexOf(elem) == pos;
+ })
+
+ return new_arr 
+};
+
+
+$.fn.getClassInList = function(list){
+  for(var i = 0; i < list.length; i++)
+  {
+    if($(this).hasClass(list[i]))
+    return list[i];
+  }
+  return "";
+}
+
+//{{{ URL PARAMETER CONTROL
+
+function add_parameters(url, parameters){
+  var string;
+
+  if ( typeof(parameters) == 'string' || typeof(parameters) == 'String'){
+    string = parameters;
+  }else{
+    var pairs = [];
+    for (parameter in parameters){
+        pairs.push(parameter + "=" + parameters[parameter]);
+    }
+    string = pairs.join("&");
+  }
+
+  if (string.length == 0){return(url)}
+
+  if (url.indexOf('?') == -1){
+    return url + '?' + string;
+  }else{
+    return url + '&' + string;
+  }
+}
+
+function remove_parameter(url, parameter){
+  if (url.match("&" + parameter)){
+    return url.replace("&" + parameter + "=", '&REMOVE=').replace(/REMOVE=[^?]+/, '').replace(/\?&/, '?').replace(/&&/, '&').replace(/[?&]$/, '');
+  }else{
+    return url.replace("?" + parameter + "=", '?REMOVE=').replace(/REMOVE=[^?]+/, '').replace(/\?&/, '?').replace(/&&/, '&').replace(/[?&]$/, '');
+  }
+}
+
+//{{{ Entity ID
+
+function id_for_entity(entity_format, entity, id){
+  if (entity_format == null){
+    return('entity_id=' + id);
+  }else{
+    return((entity_format.toLowerCase().replace(/[^\w]/g, "_") + "=" + entity));
+  }
+}
+//{{{ REPLACE OBJECTS
+
+function replace_object(obj, update, href){
+
+  if (href == null || href == undefined || href == ""){href = obj.attr('href');}
+  if (href == null || href == undefined || href == ""){href = obj.attr('target');}
+  if (href == null || href == undefined || href == ""){href = obj.attr('url');}
+
+  obj.attr('href', href);
+
+  if (update == 'reload'){
+    href = add_parameters(href, "_update=reload")
+  }
+
+  if (update == 'delete'){
+    href = add_parameters(href, "_update=delete")
+  }
+
+  if (update == 'abort'){
+    href = add_parameters(href, "_update=abort")
+  }
+
+  if (update == 'check'){
+    href = add_parameters(href, "_update=check")
+  }
+
+
+  $.ajax(href,{
+    cache: false,
+    beforeSend: function(){obj.addClass("reloading")},
+    complete: function(){
+      obj.removeClass("reloading");
+      if (update == 'delete' || update == 'abort'){
+        window.location = window.location;
+      }
+    },
+    error: function( req, text, error ) {
+      obj.removeClass("reloading");
+      obj.addClass("error");
+      if (obj.find('span[class*=status]').length == 0){
+        obj.html(obj.html() + "<span class='status'>error</status>")
+      }else{
+        obj.after($("<a class='retry_error'>retry</a>")).find('span[class*=status]').first().html("error") 
+      }
+
+      if (obj.next('a.retry_error').length == 0 && obj.next().next('a.retry_error').length == 0){
+        obj.after($("<a class='retry_error'>retry</a>"))
+        rbbt_action_setup();
+      }
+
+      obj.next('a.abort_embedded').remove();
+      obj.next().next('a.abort_embedded').remove();
+
+      rbbt_action_setup();
+    },
+    299: function( req, text, error ) {
+      obj.removeClass("reloading");
+      obj.addClass("error");
+      if (obj.find('span[class*=status]').length == 0){
+        obj.html(obj.html() + "<span class='status'>aborted</status>").after($("<a class='retry_error'>retry</a>"))
+      }else{
+        obj.after($("<a class='retry_error'>retry</a>")).find('span[class*=status]').first().html("abort") 
+      }
+      rbbt_action_setup();
+    },
+    success: function( data, stat, req ) {
+      if (req.status == 202){
+        obj.addClass("reloading");
+
+        var status_span;
+
+        if ($(data).find('span.status').length > 0){
+          status_span = "<span class='status'>" + $(data).find('span.status').html() + '</span>';
+        }else{
+          if ($('<div>').html(data).find('span.status')){
+            status_span = data;
+          }else{
+            status_span = "<span class='status'>waiting</span>";
+          }
+        }
+
+        if (obj.find('span[class*=status]').length == 0){
+          obj.html(obj.html() + status_span)
+        }else{
+          obj.find('span[class*=status]').first().replaceWith($(status_span))
+        }
+
+        if (update == 'check'){
+          obj.removeClass("reloading");
+          obj.addClass("check");
+          if (obj.find('span[class*=status]').length == 0){
+            obj.after($("<a class='start_checked'>start</a>"));
+          }else{
+            obj.after($("<a class='start_checked'>start</a>"));
+          }
+          rbbt_action_setup();
+        }else{
+
+          if (obj.next('a.abort_embedded').length == 0 && obj.next().next('a.abort_embedded').length == 0){
+            obj.after($("<a class='abort_embedded'>abort</a>"))
+            rbbt_action_setup();
+          }
+
+          window.setTimeout(function(){replace_object(obj)}, 7000)
+        }
+      }else{
+        var html = '<div class="embedded" target="' + remove_parameter(remove_parameter(req.getResponseHeader("AJAX-URL"), '_'), "_update")  + '">' + data + '</div>';
+        var embedded = $(html);
+        embedded.addClass(obj.attr('class'));
+        embedded.removeClass('replace');
+        embedded.removeClass('rbbt_action_setup');
+        embedded.removeClass("reloading");
+
+        obj.next('a.abort_embedded').remove();
+        obj.next().next('a.abort_embedded').remove();
+
+        obj.replaceWith(embedded);
+        remove_closed_section(embedded);
+        rbbt_action_setup();
+      }
+ 
+    }
+   });
+}
+
+// MISC
+
+function set_page_title(){
+  var header = $('#main header')
+
+  if (header.length > 0){
+    var title = header.first().text()
+    document.title = title
+  }
+}
+
+function contract_ellipsis(elem, max){
+  if (undefined === max) { max = 5 };
+  var text;
+  var elements;
+  var type;
+
+  if (elem.text() == elem.html()){
+    type = 'text';
+    text = elem.text();
+    elements = text.split(', ');
+  }else{
+    type = 'html';
+    elements = elem.children();
+  }
+
+  if (elements.length > max + 2){
+    if (type == 'html'){
+      elements.removeClass('rbbt_action_setup')
+    }
+    var rest = elements.length - max;
+    var ellipsis = "... (<a href=# class='open_ellipsis'>" + rest + " more</a>)";
+    var end_span = $("<span class='ellipsis' attr-text='" + escape(elem.html()) + "'>" + ellipsis + "</span>");
+    var new_content;
+    
+    if (type == 'text'){
+      new_content = elements.slice(0, max).join(", ");
+      elem.text(new_content);
+    }else{
+      var links = [];
+      var head = elements.slice(0, max);
+      head.each(function(){ links.push(this.outerHTML)})
+      new_content = links.join(", ");
+      elem.html(new_content);
+    }
+
+    end_span.appendTo(elem);
+
+    return(true);
+  }else{
+    return(false);
+  }
+}
+
+function restore_ellipsis(elem){
+  var span = elem.find('span.ellipsis')
+  if (span.length == 1){
+    var html = span.attr('attr-text');
+    elem.html(unescape(html));
+  }
+  rbbt_action_setup();
+}
+
+