rbbt-rest 1.7.20 → 1.8.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a40ff490d992383fabd6576ad3b06df0c1a9e7c4
-  data.tar.gz: d6ea9091bd3dca0e92f0628ef84b477a6e43f344
+  metadata.gz: 33b3e5b0e58772dc57de97948285d38035eccbec
+  data.tar.gz: a8b907196c822fed834fe8c7ef116b68a78ea74e
 SHA512:
-  metadata.gz: 5b813d5e2dfe4bbd36b1676a569393f7903eb8f1eb14c9392ed583991fa22cbdfea40b63f910642c5cce50610040154925aa23987855ed7c0112d15b2881754c
-  data.tar.gz: b70426b8a0d31ce739e551c23ca91ab6823aa2bc9b6036f31cf988b6327fd33bb15577ae6aef3c1c740288d46ba7139b53506df9cdb9eaad8ce8557c651aa03c
+  metadata.gz: 9b1b63cb4665226a0ece4345bec78f3cb74885ac003a1e3eb3d31f999f28060d49cc79cc490106752465af7d177b9b805c5f5ff3d7bd2a72a79509c5e7185073
+  data.tar.gz: e27f644d02bb2745e6295cb989ad4f0dfaf06dc59ed7d3f07bbe05f0049cd303560ec985819f53ddd3dc8a2ead90f1e18d413caa046001adeef6d96e5a758c2a

data/lib/rbbt/rest/common/forms.rb

@@ -99,8 +99,12 @@ module RbbtRESTHelpers
                1
              end
 
-      input_label(id, name, description, default, extra) +
-      html_tag("input", nil, html_options.merge(:type => input_type, :name => name, :value => value, :id => id, :step => step))
+      if input_type == 'hidden'
+          html_tag("input", nil, html_options.merge(:type => input_type, :name => name, :value => value, :id => id, :step => step))
+      else
+        input_label(id, name, description, default, extra) +
+          html_tag("input", nil, html_options.merge(:type => input_type, :name => name, :value => value, :id => id, :step => step))
+      end
 
     when :tsv, :array, :text, :file
       value = current.nil? ? default : current

data/lib/rbbt/rest/common/locate.rb

@@ -81,7 +81,7 @@ module RbbtRESTHelpers
   #{{{ JAVASCRIPT
 
   def self.javascript_resources
-    @javascript_resources ||= [Rbbt.share.views.public.find(:lib), Rbbt.share.views.public.js.find(:lib)]
+    @javascript_resources ||= [Rbbt.share.views.public.find(:lib), Rbbt.share.views.public.js.find(:lib), Rbbt.share.views.public.plugins.find(:lib)]
   end
 
   def javascript_resources
@@ -103,4 +103,30 @@ module RbbtRESTHelpers
 
     raise TemplateMissing, "Script #{ script } not found"
   end
+
+  #{{{ CSS
+
+  def self.css_resources
+    @css_resources ||= [Rbbt.share.views.public.find(:lib), Rbbt.share.views.public.css.find(:lib), Rbbt.share.views.public.plugins.find(:lib)]
+  end
+
+  def css_resources
+    RbbtRESTHelpers.css_resources
+  end
+
+
+  def locate_css_from_resource(resource, script)
+    path = resource[script + '.css']
+    return path if path.exists?
+    resource[script]
+  end
+ 
+  def locate_css(script)
+    css_resources.each do |resource|
+      path = locate_css_from_resource(resource, script)
+      return path if path.exists?
+    end
+
+    raise TemplateMissing, "Script #{ script } not found"
+  end
 end

data/lib/rbbt/rest/entity.rb

@@ -362,6 +362,7 @@ module Sinatra
             halt 200, TSV.open(file).to_json
           else
             map = Entity::Map.load_map(entity_type.split(":").first, column, map_id, user)
+            raise "Map not found: #{ map_id }" if map.nil?
             entity_map_render(map_id, entity_type.split(":").first, column)
           end
         end
@@ -386,7 +387,8 @@ module Sinatra
           column = Entity::REST.restore_element(params[:column])
           map_id = Entity::REST.restore_element(params[:map_id])
 
-          map = Entity::Map.load_map(entity_type.split(":").first, column, map_id, user)
+          base_type = entity_type.split(":").first
+          map = Entity::Map.load_map(base_type, column, map_id, user)
 
           Entity::Map.save_map(entity_type, column, new_id, map, user)
 
@@ -402,15 +404,18 @@ module Sinatra
 
           entity_type = consume_parameter :entity_type
           column = consume_parameter :column
+          column2 = consume_parameter :column2
           entity_type = Entity::REST.restore_element(entity_type)
           column = Entity::REST.restore_element(column)
 
           file1 = Entity::Map.map_file(entity_type.split(":").first, column, map1, user)
           file1 = Entity::Map.map_file(entity_type.split(":").first, column, map1, nil) unless File.exists? file1
-          tsv1 =  TSV.open(file1)
+          raise "Map not found: #{ map1 }" unless File.exists? file1
+          tsv1 =  TSV.open(file1) 
 
-          file2 = Entity::Map.map_file(entity_type.split(":").first, column, map2, user)
-          file2 = Entity::Map.map_file(entity_type.split(":").first, column, map2, nil) unless File.exists? file2
+          file2 = Entity::Map.map_file(entity_type.split(":").first, column2, map2, user)
+          file2 = Entity::Map.map_file(entity_type.split(":").first, column2, map2, nil) unless File.exists? file2
+          raise "Map not found: #{ map2 } - #{ file2 }" unless File.exists? file2
           tsv2 =  TSV.open(file2)
 
           tsv1.attach tsv2, :fields => tsv2.fields

data/lib/rbbt/rest/entity/locate.rb

@@ -8,6 +8,32 @@ module EntityRESTHelpers
     [Rbbt.share.views.find(:lib)] +  EntityRESTHelpers.entity_resources
   end
  
+  #{{{ CHECKS
+
+  def reject_template(path,binding)
+    check_file = path.sub(/\.haml$/, '.check')
+
+    if Path === path
+      path.annotate check_file 
+      return false unless check_file.exists?
+    else
+      return false unless File.exists?(check_file)
+    end
+
+    begin
+      code = Open.read(check_file)
+      accept = eval code, binding, check_file, 0
+      Log.debug{"Checking action template: #{path} - #{accept ? 'accepted' : 'rejected'}"}
+      return ! accept
+    rescue 
+      Log.exception $!
+      iii path
+      ppp code
+      return true
+    end
+    false
+  end
+
   #{{{ ENTITY
 
   def locate_entity_template_from_resource(resource, entity)
@@ -54,59 +80,10 @@ module EntityRESTHelpers
 
   #{{{ ENTITY ACTION
 
-  def find_all_entity_action_templates_from_resource(resource, entity)
-    if entity == "Default" 
-      resource.entity["Default"].glob("*.haml").sort
-    else
-      entity.annotation_types.collect do |annotation|
-        resource.entity[annotation].glob('*.haml')
-      end.compact.flatten.sort
-    end
-  end   
-
-  def find_all_entity_action_templates(entity, check = false)
-    paths = []
-
-    if entity.respond_to? :dir and Path === entity.dir
-      paths.concat find_all_entity_action_templates_from_resource(entity.dir.www.views, entity)
-    end
-
-    entity_resources.each do |resource|
-      paths.concat find_all_entity_action_templates_from_resource(resource, entity)
-    end
-
-    entity_resources.each do |resource|
-      paths.concat find_all_entity_action_templates_from_resource(resource, "Default")
-    end
-
-    if check
-      paths = paths.reject do |path|
-        check_file = path.sub(/\.haml$/, '.check')
-        case
-        when (path.basename == "edit.haml" or path.basename == 'new.haml')
-          true
-        when File.exists?(check_file)
-          begin
-            Log.debug{"Checking action template: #{path}"}
-            code = File.read(check_file)
-            accept = eval code
-            not accept
-          rescue
-            Log.debug{"Error Checking action template #{path}: #{$!.message}"}
-            true
-          end
-        else
-          false
-        end
-      end
-    end
-
-    paths.collect{|file| file.basename.sub('.haml', '') }.uniq
-  end
-
   def locate_entity_action_template_from_resource(resource, entity, action)
     if entity == "Default" 
       path = resource.entity["Default"][action.to_s + ".haml"]
+      raise "This action was rejected: #{ action }" if path and reject_template(path,binding)
       if path.exists?
         return path
       else
@@ -116,6 +93,7 @@ module EntityRESTHelpers
 
     entity.annotation_types.each do |annotation|
       path = resource.entity[annotation][action.to_s + ".haml"]
+      raise "This action was rejected: #{ action }" if path and reject_template(path,binding)
       return path if path.exists?
     end
 
@@ -136,12 +114,56 @@ module EntityRESTHelpers
 
     entity_resources.each do |resource|
       path = locate_entity_action_template_from_resource(resource, "Default", action)
+      raise "This action was rejected: #{ action }" if reject_template(path,binding)
       return path if path and path.exists?
     end
 
     raise "Template not found for action #{action}: #{ entity } (#{entity.annotation_types * ", "})"
   end
 
+  def find_all_entity_action_templates_from_resource(resource, entity)
+    if entity == "Default" 
+      resource.entity["Default"].glob("*.haml").sort
+    else
+      entity.annotation_types.collect do |annotation|
+        resource.entity[annotation].glob('*.haml')
+      end.compact.flatten.sort
+    end
+  end   
+
+  def find_all_entity_action_templates(entity, check = false)
+    paths = []
+
+    if entity.respond_to? :dir and Path === entity.dir
+      paths.concat find_all_entity_action_templates_from_resource(entity.dir.www.views, entity)
+    end
+
+    entity_resources.each do |resource|
+      paths.concat find_all_entity_action_templates_from_resource(resource, entity)
+    end
+
+    entity_resources.each do |resource|
+      paths.concat find_all_entity_action_templates_from_resource(resource, "Default")
+    end
+
+    if check
+      paths = paths.reject do |path|
+        (path.basename == "edit.haml" or path.basename == 'new.haml') 
+      end
+    end
+
+    actions = paths.collect{|file| file.basename.sub('.haml', '') }.uniq
+
+    actions.select! do |action|
+      begin
+        locate_entity_action_template(entity, action)
+      rescue Exception
+        false
+      end
+    end if check
+    
+    actions
+  end
   #{{{ ENTITY LIST
 
   def locate_entity_list_template_from_resource(resource, list)
@@ -189,61 +211,11 @@ module EntityRESTHelpers
 
   #{{{ ENTITY LIST ACTION
  
-  def find_all_entity_list_action_templates_from_resource(resource, entity)
-
-    if entity == "Default" 
-      resource.entity_list["Default"].glob("*.haml").sort
-    else
-      entity.annotation_types.collect do |annotation|
-        resource.entity_list[annotation].glob('*.haml')
-      end.compact.flatten.sort
-    end
-  end   
-
-  def find_all_entity_list_action_templates(list, check = false)
-    paths = []
-
-    if list.respond_to? :dir and Path === list.dir
-      paths.concat find_all_entity_list_action_templates_from_resource(list.dir.www.views, list)
-    end
-
-    entity_resources.each do |resource|
-      paths.concat find_all_entity_list_action_templates_from_resource(resource, list)
-    end
-
-    entity_resources.each do |resource|
-      paths.concat find_all_entity_list_action_templates_from_resource(resource, "Default")
-    end
-
-    if check
-      paths = paths.reject do |path|
-        check_file = path.sub(/\.haml$/, '.check')
-        case
-        when (path.basename == "edit.haml" or path.basename == 'new.haml')
-          true
-        when File.exists?(check_file)
-          begin
-            Log.debug{ "Checking action template: #{path}" }
-            code = File.read(check_file)
-            accept = eval code
-            not accept
-          rescue
-            Log.debug{ "Error Checking action template #{path}: #{$!.message}" }
-            true
-          end
-        else
-          false
-        end
-      end
-    end
-
-    paths.collect{|file| file.basename.sub('.haml', '') }.uniq
-  end
-
  
   def locate_entity_list_action_template_from_resource(resource, list, action)
     if list == "Default" 
       path = resource.entity_list["Default"][action.to_s + ".haml"]
+      raise "This action was rejected: #{ action }" if path and reject_template(path,binding)
       if path.exists?
         return path
       else
@@ -253,6 +225,7 @@ module EntityRESTHelpers
 
     list.annotation_types.each do |annotation|
       path = resource.entity_list[annotation][action.to_s + ".haml"]
+      raise "This action was rejected: #{ action }" if path and reject_template(path,binding)
       return path if path.exists?
     end
 
@@ -279,6 +252,51 @@ module EntityRESTHelpers
     raise "Template not found for list #{ action } (#{list.annotation_types * ", "})"
   end
 
+  def find_all_entity_list_action_templates_from_resource(resource, entity)
+
+    if entity == "Default" 
+      resource.entity_list["Default"].glob("*.haml").sort
+    else
+      entity.annotation_types.collect do |annotation|
+        resource.entity_list[annotation].glob('*.haml')
+      end.compact.flatten.sort
+    end
+  end   
+
+  def find_all_entity_list_action_templates(list, check = false)
+    paths = []
+
+    if list.respond_to? :dir and Path === list.dir
+      paths.concat find_all_entity_list_action_templates_from_resource(list.dir.www.views, list)
+    end
+
+    entity_resources.each do |resource|
+      paths.concat find_all_entity_list_action_templates_from_resource(resource, list)
+    end
+
+    entity_resources.each do |resource|
+      paths.concat find_all_entity_list_action_templates_from_resource(resource, "Default")
+    end
+
+    if check
+      paths = paths.reject do |path|
+        (path.basename == "edit.haml" or path.basename == 'new.haml') 
+      end
+    end
+
+    actions = paths.collect{|file| file.basename.sub('.haml', '') }.uniq
+
+    actions.select! do |action|
+      begin
+        locate_entity_list_action_template(list, action)
+      rescue Exception
+        false
+      end
+    end if check
+    
+    actions
+  end
+
   #{{{ ENTITY MAP
 
   def locate_entity_map_template_from_resource(resource, type)
@@ -314,7 +332,7 @@ module EntityRESTHelpers
 
   #{{{ ENTITY MAP ACTION
  
-  def find_all_entity_map_action_templates_from_resource(resource, map)
+  def locate_entity_map_action_template_from_resource(resource, map, action)
     field = map.key_field
 
     if map.entity_templates[field] 
@@ -325,45 +343,26 @@ module EntityRESTHelpers
 
     annotation_types += ["Default"]
 
-    annotation_types.collect do |annotation|
-      resource.entity_map[annotation].glob('*.haml')
-    end.compact.flatten
+    annotation_types.each do |annotation|
+      path = resource.entity_map[annotation][action.to_s + ".haml"]
+      raise "This action was rejected: #{ action }" if path and reject_template(path,binding)
+      return path if path.exists?
+    end
+
+    nil
   end   
 
-  def find_all_entity_map_action_templates(map, check = false)
-    paths = []
+  def locate_entity_map_action_template(map, action)
 
     entity_resources.each do |resource|
-      paths.concat find_all_entity_map_action_templates_from_resource(resource, map)
-    end
-
-    if check
-      paths = paths.reject do |path|
-        check_file = path.sub(/\.haml$/, '.check')
-        case
-        when (path.basename == "edit.haml" or path.basename == 'new.haml')
-          true
-        when File.exists?(check_file)
-          begin
-            Log.debug{ "Checking action template: #{path}" }
-            code = File.read(check_file)
-            accept = eval code
-            not accept
-          rescue
-            Log.debug{ "Error Checking action template #{path}: #{$!.message}" }
-            true
-          end
-        else
-          false
-        end
-      end
+      path = locate_entity_map_action_template_from_resource(resource, map, action)
+      return path if path and path.exists?
     end
 
-    paths.collect{|file| file.basename.sub('.haml', '') }.uniq
+    raise "Template not found for map #{ action } (#{map.key_field * ", "})"
   end
 
- 
-  def locate_entity_map_action_template_from_resource(resource, map, action)
+  def find_all_entity_map_action_templates_from_resource(resource, map)
     field = map.key_field
 
     if map.entity_templates[field] 
@@ -374,22 +373,36 @@ module EntityRESTHelpers
 
     annotation_types += ["Default"]
 
-    annotation_types.each do |annotation|
-      path = resource.entity_map[annotation][action.to_s + ".haml"]
-      return path if path.exists?
-    end
-
-    nil
+    annotation_types.collect do |annotation|
+      resource.entity_map[annotation].glob('*.haml')
+    end.compact.flatten
   end   
 
-  def locate_entity_map_action_template(map, action)
+  def find_all_entity_map_action_templates(map, check = false)
+    paths = []
 
     entity_resources.each do |resource|
-      path = locate_entity_map_action_template_from_resource(resource, map, action)
-      return path if path and path.exists?
+      paths.concat find_all_entity_map_action_templates_from_resource(resource, map)
     end
 
-    raise "Template not found for map #{ action } (#{map.key_field * ", "})"
+    if check
+      paths = paths.reject do |path|
+        (path.basename == "edit.haml" or path.basename == 'new.haml')
+      end
+    end
+
+    actions = paths.collect{|file| file.basename.sub('.haml', '') }.uniq
+
+    actions.select! do |action|
+      begin
+        locate_entity_map_action_template(map, action)
+      rescue Exception
+        false
+      end
+    end if check
+    
+    actions
   end
 
+ 
 end

data/lib/rbbt/rest/entity/rest.rb

@@ -14,11 +14,11 @@ module Entity
     #{{{ MISC
     
     def self.clean_element(elem)
-      elem.gsub('/', '--').gsub('%', 'o-o')
+      elem.gsub('/', '-..-').gsub('%', 'o-o').gsub('[','(.-(').gsub(']',').-)')
     end
  
     def self.restore_element(elem)
-      CGI.unescape(CGI.unescape(elem.gsub('--', '/').gsub('o-o', '%')))
+      CGI.unescape(CGI.unescape(elem.gsub('-..-', '/').gsub('o-o', '%').gsub('(.-(','[').gsub(').-)',']')))
     end
 
     def entity_link_params

data/lib/rbbt/rest/main.rb

@@ -27,7 +27,10 @@ module Sinatra
 
       RbbtRESTHelpers.add_sass_load_path path.compass if path.compass.exists?
 
-      RbbtRESTHelpers.javascript_resources.unshift path.public.js if path.public.js.exists?
+      RbbtRESTHelpers.javascript_resources.unshift path.public.js if path.public.js.exists? 
+      RbbtRESTHelpers.css_resources.unshift path.public.css if path.public.css.exists? 
+      RbbtRESTHelpers.javascript_resources.unshift path.public.plugins if path.public.plugins.exists? 
+      RbbtRESTHelpers.css_resources.unshift path.public.plugins if path.public.plugins.exists? 
       RbbtRESTHelpers.sass_resources.unshift path.compass if path.compass.exists?
     end
 
@@ -140,6 +143,17 @@ module Sinatra
           send_file script_file
         end
 
+        get %r{/css-find/(.*)(.css)?} do
+          name = consume_parameter(:captures).first
+
+          script_file = locate_css(name)
+
+          content_type 'text/css', :charset => 'utf-8' if script_file =~ /\.js$/
+          cache_control :public, :max_age => 360000 if production?
+          send_file script_file
+        end
+
+
         get '/stylesheets/*' do
           name = consume_parameter :splat
 

data/share/views/compass/app.sass

@@ -47,3 +47,6 @@ a.entity
 
 table > caption
   max-width: 60em
+
+.filters + p
+  margin-top: 2em

data/share/views/entity_partials/entity_map_card.haml

@@ -14,13 +14,13 @@
     .info.ui.compact.segment
       .meta
         .map_management.ui.buttons
-          = reveal "Rename", nil, :class => 'ui small button' do
-            %form.rename
+          = reveal "Rename", nil, :class => 'ui small button rename_map' do
+            %form.rename_map
               %label New name
               %input(name='rename' value=map_id)
               %input(type='submit')
 
-          - if %w(pvalue p.value p-value pvalues p.values p-values qvalue q.value q-value qvalues q.values q-values).include? map.fields.first.downcase.gsub(/\s/,'')
+          - if (%w(pvalue p.value p-value pvalues p.values p-values qvalue q.value q-value qvalues q.values q-values) & map.fields.first.downcase.split(/\s+/)).any? and map.fields.first.downcase !~ /score$/
             - url = add_GET_param(@fullpath, '_format', 'pvalue_score')
             %a.ui.small.button(href=url) Pvalue score
 
@@ -40,15 +40,19 @@
           - if NumericValue == Entity.formats[map.fields.first] or (map.entity_templates[map.fields.first] and map.entity_templates[map.fields.first].annotation_types.include? NumericValue)
             - $page_entity_base_type = page_entity_base_type 
             - $page_entity_map_column = page_entity_map_column 
-            = reveal :rank_products, nil, :title => "Rank Product", :class => 'ui small button' do
+            = reveal "Rank products", nil, :class => 'ui small button rank_product' do
               = action_parameters nil, :class => 'rank_products' do
                 - input :map, :select, "Select map to use", nil, :html_options => {:class => 'favourite_maps', :type =>  $page_entity_base_type, :column => $page_entity_map_column}
 
+            = reveal "Compare plot", nil, :class => 'ui small button plot' do
+              = action_parameters nil, :class => 'plot' do
+                - input :map, :select, "Select map to use", nil, :html_options => {:class => 'favourite_maps', :type =>  $page_entity_base_type, :column => $page_entity_map_column}
+
 
 
     .content
       .description
-        = table :class => 'ui collapsing table' do
+        = table :class => 'ui collapsing table', :table_id => map_id do
           - map
       - if card.action_controller
         .actions

data/share/views/layout/coda.haml

@@ -11,6 +11,7 @@
 
   var known_types = #{Entity::REST::REST_ENTITIES.collect{|m| m.to_s}.to_json}
 
+-#
   function gene_name(name){
     return new Entity({type: "Gene", id: name, name: name, format: "Associated Gene Name", info: { organism: "Hsa/feb2014" }})
   }

data/share/views/partials/table/filters.haml

@@ -16,10 +16,10 @@
   :markdown
     Filters can be specified in several ways:
 
-      - *String of text*: perfect match (e.g. `Cancer`)
-      - *Regular expression*: flexible match (e.g. `/(bladder|breast)\s+cancer/i`)
-      - *Numeric comparison*: lower of grater than (e.g. `< 0.1` or `>= 2`)
-      - *Names*: for entities with names, such as genes or pathways; regular expression accepted (e.g. `:name: SF3B1` or `:name: /CDK\d/`)
-      - *Length*: for lists (e.g. `:length: > 2`)
-      - *Negation*: Any of the rules above can be negated by prepending the `!` character (e.g. `!:name:/^IG/`)
+      - *String of text*: perfect match (e.g. `'Cancer'`)
+      - *Regular expression*: flexible match (e.g. `'/(bladder|breast)\s+cancer/i'`)
+      - *Numeric comparison*: lower of grater than (e.g. `'< 0.1'` or `'>= 2'`)
+      - *Names*: for entities having 'human-friendly' names, such as genes or pathways; regular expression accepted (e.g. `':name: SF3B1'` or `':name: /CDK\d/'`)
+      - *Length*: for lists (e.g. `':length: > 2'`)
+      - *Negation*: Any of the rules above can be negated by prepending the `!` character (e.g. `'!:name:/^IG/'`)
 

data/share/views/public/js/helpers/helpers.js

@@ -37,11 +37,11 @@ function remove_parameter(url, parameter){
 }
 
 function clean_element(elem){
- return elem.replace(/\//g, '--').replace(/%/g,'o-o')
+ return elem.replace(/\//g, '-..-').replace(/%/g,'o-o').replace(/\[/g,'(.-(').replace(/\]/g,').-)')
 }
 
 function restore_element(elem){
- return unescape(elem.replace(/--/g, '/').replace(/o-o/g,'%'));
+ return unescape(elem.replace(/-\.\.-/g, '/').replace(/o-o/g,'%')).replace(/\(\.-\(/g,'[').replace(/\)\.-\)/g,']');
 }
 
 function parse_parameters(params){
@@ -70,7 +70,7 @@ function require_js(url, success, script){
    }
  }else{
   var async = true;
-  if (undefined === production) production = false
+  if (typeof production == 'undefined') production = false
   var cache = production;
 
   if (undefined === success){
@@ -79,12 +79,14 @@ function require_js(url, success, script){
    async = true;
   }
 
-  url = url.replace('/js/', '/js-find/')
+  url = url.replace('^/js/', '/js-find/')
 
   if ($.inArray(url, required_js) >= 0){
     if (typeof success == 'function'){ success.call(script) }
   }else{
-    var _success = function(){ required_js.push(url); if (typeof success == 'function'){ success.call(script) }; }
+    var _success = function(script_text){ required_js.push(url); console.log("Required and loaded JS: " + url); if (typeof success == 'function'){ success(script) }; }
+    if (typeof rbbt.proxy != 'undefined')
+      url = rbbt.proxy + url
     $.ajax({url: url, cache:cache, dataType:'script', async: async, success: _success} ).fail(function(jqxhr, settings, exception){ console.log('Failed to load ' + url) })
   }
  }

data/share/views/public/js/rbbt.entity_list.js

@@ -142,7 +142,11 @@ FavouriteLists.get = function(){
 }
 
 FavouriteLists.deserialize = function(data){
-  data = JSON.parse(data)
+  try{
+    data = JSON.parse(data)
+  }catch(err){
+    data = {}
+  }
   favourite_lists = {}
 
   forHash(data, function(type, type_data){

data/share/views/public/js/rbbt.plots/rbbt.plots.aes.js

@@ -39,6 +39,7 @@ rbbt.plots.aes.map_aesthetic = function(aes, mapper, map_obj){
       return map_obj(aes)
   }
 }
+
 rbbt.plots.aes.get_properties = function(list, rules){
   if (undefined === rules) rules == []
   if (undefined === list.properties) list.properties = {}
@@ -190,6 +191,17 @@ rbbt.plots.aes.set_aes = function(list, aes_rules){
     if (undefined === property && name == 'code') property = list.codes
     if (undefined === property) return
 
-    list.aes[aes] = rbbt.plots.aes.map_aesthetic(property, mapper, mapper_obj)
+    var aes_values = rbbt.plots.aes.map_aesthetic(property, mapper, mapper_obj)
+
+    if (undefined === list.aes[aes]){
+      list.aes[aes] = aes_values
+    }else{
+      for(i in aes_values){
+        var v = aes_values[i]
+        if (undefined !== v){
+          list.aes[aes][i] = v
+        }
+      }
+    }
   })
 }

data/share/views/public/js/rbbt.plots/rbbt.plots.graph.adapters.js

@@ -110,7 +110,6 @@ rbbt.plots.graph.view_cytoscapejs = function(graph_model, elem, style, layout, e
 
   var deferred = m.deferred()
 
-  console.log(graph_model)
   rbbt.plots.graph.update(graph_model).then(function(updated_model){
     var cy_model = rbbt.plots.graph.build_cytoscapejs(updated_model)
 

data/share/views/public/js/rbbt/list.js

@@ -121,7 +121,7 @@ body.on('click', '.edit_list input[type=submit]', function(){
 
   if (undefined !== format){ entity_type = entity_type + ':' + clean_element(format) }
 
-  var url = '/entity_list/' + entity_type + '/' + new_list_id  
+  var url = '/entity_list/' + clean_element(entity_type) + '/' + clean_element(new_list_id  )
 
   get_ajax({url: url, type: 'POST', async: false, data: {annotations: JSON.stringify(annotations), entities: entities}}, function(){ window.location = url })
 

data/share/views/public/js/rbbt/map.js

@@ -1,18 +1,116 @@
 function entity_map(type, column, id, complete){
   var url = "/entity_map" + '/' + clean_element(type) + '/' + clean_element(column) + '/' + clean_element(id);
-  return get_ajax({url: url, async: false, method: "GET", data: {_format: 'json'}}, complete)
+  return rbbt.ajax({url: url, async: false, method: "GET", data: {_format: 'json'}}, complete)
 }
 
+$('body').on('click', '#modal form.rename_map input[type=submit]', function(){
+  console.log(1)
+  var map = rbbt.page.map();
+  var map_id = map.id
+
+  var submit = $(this);
+  var input = submit.closest('form').find('input[name=rename]')
+  var new_name = input.val();
+  var entity_type = map.type
+  var column = map.column
+  url = '/entity_map/rename/'+ clean_element(entity_type) + '/'+ clean_element(column) +'/' + clean_element(map_id) + '?new_name=' + clean_element(new_name)
+  window.location = url
+  return false
+})
+
 $('body').on('click', '.rank_products form input[type=submit]', function(){
-  var map1 = page_entity_map();
+  var map = rbbt.page.map();
+  var map1 = map.id;
 
   var input = $(this);
   var select = input.closest('form').find('select')
   var map2 = select.val();
-  var entity_type = page_entity_base_type()
-  var column = page_entity_map_column()
-  url = "/entity_map/rank_products?map1=" + clean_element(map1) + "&map2=" + clean_element(map2) + '&entity_type=' + entity_type + "&column=" + column
+  var entity_type = map.type
+  var column = map.column
+  var column2 = select.find('option:selected').attr('attr-column')
+  url = "/entity_map/rank_products?map1=" + clean_element(map1) + "&map2=" + clean_element(map2) + '&entity_type=' + entity_type + "&column=" + column +  "&column2=" + column2
   window.location = url
   return false
 })
 
+$('body').on('click', '.plot form input[type=submit]', function(){
+  var map = rbbt.page.map();
+  var map1 = map.id;
+
+  var input = $(this);
+  var select = input.closest('form').find('select')
+  var map2 = select.val();
+  var entity_type = map.type
+  var column = map.column
+  var column2 = select.find('option:selected').attr('attr-column')
+
+  m.sync([entity_map(entity_type,column,map1), entity_map(entity_type,column2, map2)]).then(function(res){
+    var modal = $('#modal')
+    var container = $('<div>').addClass('plot_container')
+
+    var res1, res2
+    res1 = res[0]
+    res2 = res[1]
+
+    var tmp_data = []
+    forHash(res1,function(k,v1){
+      var v2 = res2[k]
+      if (undefined !== v2)
+        tmp_data.push([v1,v2,k])
+    })
+    tmp_data = tmp_data.sort(function(a,b){ return a[0] - b[0] })
+
+    var data = []
+    var keys = []
+
+    for(i in tmp_data){
+      var k,v1,v2 
+      v1 = tmp_data[i][0]
+      v2 = tmp_data[i][1]
+      k = tmp_data[i][2]
+
+      keys.push(k)
+      data.push([v1,v2])
+    }
+
+    require_js('https://code.highcharts.com/highcharts.js', function(){
+         container.highcharts({
+        title: {
+            text: map1 + ' vs. ' + map2,
+            x: -20 //center
+        },
+        subtitle: {
+            text: 'Comparison plot',
+            x: -20
+        },
+        xAxis: {
+            title: {
+                text: map1 + ': ' + column
+            },
+        },
+        yAxis: {
+            title: {
+                text: map2 + ': ' + column2
+            },
+        },
+        legend: {
+            layout: 'vertical',
+            align: 'right',
+            verticalAlign: 'middle',
+            borderWidth: 0
+        },
+        series: [{
+            name: 'Comparison',
+            data: data,
+            labels: keys,
+        }]
+    });
+
+    modal.find('.content').append(container)
+ 
+    })
+  })
+
+  return false
+})
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.7.20
+  version: 1.8.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-14 00:00:00.000000000 Z
+date: 2016-03-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake