rbbt-rest 1.5.0 → 1.6.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 373227cb24541cc0b77e52a7228c1e8b4f7dafc8
-  data.tar.gz: f4fcde8a61a88c37f99e4e3ab64cc2b413eba217
+  metadata.gz: 019b238df0884dac2b1bd0c4c97588d9c0ddf295
+  data.tar.gz: dbb37b58e7d10dc8a2fd82e4636eb006427733fe
 SHA512:
-  metadata.gz: f1f78d6a708dee3e21eea2cfe7825d951babf1bb6f226322a33fd1ad36245787344e205bd45c2b5730bb0d471f33c579c834052b12e32e05f585440b6dcc4f42
-  data.tar.gz: 1fb872b28cffc3bf7b656fbde9318fb201193bdcf811390327524d277cd15ad8dc3826befde3bea35d76f5372375a501bcf92f52ec0d3240cac804b5b1e0b696
+  metadata.gz: 3645c2891ebaf8ccbfd1afd8a938b3b2e1a186fe3f6115b53cd62d978337293da74524065d9d25624e96207b5adecea1f70f90d1bac2bda4a157f2c9b2d91b8e
+  data.tar.gz: 5eb156ff821ac00db1b6ddd0949ff4e7f9e85e2161e97b1a52cf408ad4f27baab472b463b972a2775764ba7da67b58d77c81651e58b4fa9db0c9776d7ad08a8d

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

@@ -41,6 +41,36 @@ module RbbtRESTHelpers
       send_file step.file(@file), :filename => @file
     end
 
+    # Clean/update job
+
+    if old_cache(step.path, check) or update == :reload
+      begin
+        pid = step.info[:pid] 
+        step.abort if pid and Misc.pid_exists?(pid) and not pid == Process.pid
+        step.pid = nil
+      rescue Exception
+        Log.medium{$!.message}
+      end
+      step.clean 
+    end
+
+    clean_url = request.url
+    clean_url = remove_GET_param(clean_url, :_update)
+    clean_url = remove_GET_param(clean_url, :_)
+
+    class << step; def url; @url; end; end
+    step.instance_variable_set(:@url, clean_url)
+
+    # Issue
+    if not step.started?
+      if cache_type == :synchronous or cache_type == :sync
+        step.run 
+      else
+        step.fork
+        step.soft_grace
+      end
+    end
+
     # Return fragment
 
     if @fragment
@@ -68,7 +98,9 @@ module RbbtRESTHelpers
           list_id << " (#{ @filter })" if @filter
           Entity::List.save_list(type.to_s, list_id, list, user)
           header "Location", Entity::REST.entity_list_url(list_id, type)
-          redirect to(Entity::REST.entity_list_url(list_id, type))
+          url = Entity::REST.entity_list_url(list_id, type)
+          url = url + '?_layout=false' unless @layout
+          redirect to(url)
         when "map"
           tsv = tsv_process(load_tsv(fragment_file).first)
           type = tsv.keys.annotation_types.last
@@ -77,6 +109,7 @@ module RbbtRESTHelpers
           map_id << " (#{ @filter.gsub(';','|') })" if @filter
           Entity::Map.save_map(type.to_s, column, map_id, tsv, user)
           url = Entity::REST.entity_map_url(map_id, type, column)
+          url = url + '?_layout=false' unless @layout
           redirect to(url)
         when "excel"
           require 'rbbt/tsv/excel'
@@ -101,36 +134,6 @@ module RbbtRESTHelpers
       end
     end
 
-    # Clean/update job
-
-    if old_cache(step.path, check) or update == :reload
-      begin
-        pid = step.info[:pid] 
-        step.abort if pid and Misc.pid_exists?(pid) and not pid == Process.pid
-        step.pid = nil
-      rescue Exception
-        Log.medium{$!.message}
-      end
-      step.clean 
-    end
-
-    clean_url = request.url
-    clean_url = remove_GET_param(clean_url, :_update)
-    clean_url = remove_GET_param(clean_url, :_)
-
-    class << step; def url; @url; end; end
-    step.instance_variable_set(:@url, clean_url)
-
-    # Issue
-    if not step.started?
-      if cache_type == :synchronous or cache_type == :sync
-        step.run 
-      else
-        step.fork
-        step.soft_grace
-      end
-    end
-
     if update == :reload
       redirect to(clean_url)
     end

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

@@ -346,6 +346,7 @@ module RbbtRESTHelpers
 
       url = add_GET_param(@fullpath, "_fragment", File.basename(table_file))
       url = remove_GET_param(url, "_update")
+      url = remove_GET_param(url, "_layout")
       url = remove_GET_param(url, "_")
     end
 

data/lib/rbbt/rest/entity.rb

@@ -305,7 +305,8 @@ module Sinatra
           when :name
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
-            new = TSVWorkflow.job(:change_id, "Map #{ map_id }", :format => "Associated Gene Name", :tsv => TSV.open(file)).exec
+            #new = TSVWorkflow.job(:swap_id, "Map #{ map_id }", :format => "Associated Gene Name", :tsv => TSV.open(file)).exec
+            new = TSV.open(file).change_key "Associated Gene Name"
             new_id = map_id << " [Names]"
             Entity::Map.save_map(entity_type, column, new_id, new, user)
             redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
@@ -484,7 +485,8 @@ module Sinatra
               next unless entity.respond_to? :link
               info = entity.info
               info.delete :annotation_types
-              type_favs[entity] = {:info => info, :link => entity.link} 
+              default = entity.respond_to?(:default) ? entity.default || entity.to_s : entity.to_s
+              type_favs[entity] = {:info => info, :link => entity.link, :code => entity, :id => default, :name => (entity.respond_to?(:name) ? entity.name || entity : entity) } 
             end
             favs[type] = type_favs
           }

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

@@ -139,7 +139,7 @@ module EntityRESTHelpers
 
     dir = Path.setup(File.join(settings.favourite_maps_dir, user))
 
-    if (file = dir[entity_type][column]).exists?
+    if (file = dir[entity_type][column].find).exists?
       maps = Open.read(file).split("\n")
       maps -= [map]
       if maps.any?

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

@@ -131,6 +131,10 @@ module Entity
       attributes[:href] = Entity::REST.entity_url(self, entity_type.to_s, link_params)
       attributes["attr-entity_id"] = self.to_s
 
+      attributes["data-entity-type"] = self.base_type
+      attributes["data-entity"] = self.to_s
+      attributes["data-entity-id"] = self.respond_to?(:default)? self.default || self.to_s : self.to_s
+
       begin
         text = self.respond_to?(:name)? self.name || self : self if text.nil?
       rescue
@@ -191,8 +195,8 @@ module Entity
     end
 
     def list_action_link(action, text = nil, id = nil, options = {})
-      text = [id, action] * "→" if text.nil? or (String === text and text.strip.empty?)
       id = options[:id] || Misc.digest((self * "|").inspect) if id.nil? or (String === id and id.empty?)
+      text = [id, action] * "→" if text.nil? or (String === text and text.strip.empty?)
 
       reuse = options.delete(:reuse)
       reuse = options.delete("reuse") if reuse.nil?

data/lib/rbbt/rest/knowledge_base.rb

@@ -111,344 +111,376 @@ module Sinatra
           else
             content_type :text
             halt 200, subset.source * "\n"
-    end
-  end
+          end
+        end
 
 
-  #{{{ Collection
+        #{{{ Collection
 
-  post '/knowledge_base/:name/:database/collection_children' do 
-    name = consume_parameter :name
-    database = consume_parameter :database
-    collection = consume_parameter :collection 
-    raise ParameterException, "No collection specified" if collection.nil?
-    collection = JSON.parse(collection)
+        post '/knowledge_base/:name/:database/collection_children' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          collection = consume_parameter :collection 
+          raise ParameterException, "No collection specified" if collection.nil?
+          collection = JSON.parse(collection)
 
-    kb = get_knowledge_base name
-    matches = collection.keys.inject({}){|acc,type|
-      entities = collection[type]
-      entities.each do |entity|
-        _matches = kb.children(database, entity)
-        acc.merge!({ _matches.target_type => _matches}) if _matches and _matches.any?
-      end
-      acc
-    }
-    case @format
-    when :tsv
-      content_type "text/tab-separated-values"
-      matches = matches.sort_by{|k,list| list.length }.last.last
-      halt 200, matches.tsv.to_s
-    when :html
-      template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Children: #{ [name, database] }")
-    when :json
-      content_type :json
-      _matches = {}
-      matches.each{|type,list|
-        _matches[type] = list.target
-      }
-      halt 200, _matches.to_json
-    else
-      content_type :text
-      matches = matches.sort_by{|k,list| list.length }.last.last
-      halt 200, matches.target * "\n"
-    end
-  end
+          kb = get_knowledge_base name
+          matches = collection.keys.inject({}){|acc,type|
+            entities = collection[type]
+            entities.each do |entity|
+              _matches = kb.children(database, entity)
+              acc.merge!({ _matches.target_type => _matches}) if _matches and _matches.any?
+            end
+            acc
+          }
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Children: #{ [name, database] }")
+          when :json
+            content_type :json
+            _matches = {}
+            matches.each{|type,list|
+              _matches[type] = list.target
+            }
+            halt 200, _matches.to_json
+          else
+            content_type :text
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.target * "\n"
+          end
+        end
 
-  post '/knowledge_base/:name/:database/collection_parents' do 
-    name = consume_parameter :name
-    database = consume_parameter :database
-    collection = consume_parameter :collection 
-    raise ParameterException, "No collection specified" if collection.nil?
-    collection = JSON.parse(collection)
-
-    kb = get_knowledge_base name
-    matches = collection.keys.inject({}){|acc,type|
-      entities = collection[type]
-      entities.each do |entity|
-        _matches = kb.parents(database, entity)
-        acc.merge!({ _matches.target_type => _matches}) if _matches and _matches.any?
-      end
-      acc
-    }
-    case @format
-    when :tsv
-      content_type "text/tab-separated-values"
-      matches = matches.sort_by{|k,list| list.length }.last.last
-      halt 200, matches.tsv.to_s
-    when :html
-      template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Parents: #{ [name, database] }")
-    when :json
-      content_type :json
-      _matches = {}
-      matches.each{|type,list|
-        _matches[type] = list.target
-      }
-      halt 200, _matches.to_json
-    else
-      content_type :text
-      matches = matches.sort_by{|k,list| list.length }.last.last
-      halt 200, matches.target * "\n"
-    end
-  end
+        post '/knowledge_base/:name/:database/collection_parents' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          collection = consume_parameter :collection 
+          raise ParameterException, "No collection specified" if collection.nil?
+          collection = JSON.parse(collection)
+
+          kb = get_knowledge_base name
+          matches = collection.keys.inject({}){|acc,type|
+            entities = collection[type]
+            entities.each do |entity|
+              _matches = kb.parents(database, entity)
+              acc.merge!({ _matches.target_type => _matches}) if _matches and _matches.any?
+            end
+            acc
+          }
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Parents: #{ [name, database] }")
+          when :json
+            content_type :json
+            _matches = {}
+            matches.each{|type,list|
+              _matches[type] = list.target
+            }
+            halt 200, _matches.to_json
+          else
+            content_type :text
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.target * "\n"
+          end
+        end
+
+        post '/knowledge_base/:name/:database/collection_neighbours' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          collection = consume_parameter :collection 
+          raise ParameterException, "No collection specified" if collection.nil?
+          collection = JSON.parse(collection)
 
-  post '/knowledge_base/:name/:database/collection_neighbours' do 
-    name = consume_parameter :name
-    database = consume_parameter :database
-    collection = consume_parameter :collection 
-    raise ParameterException, "No collection specified" if collection.nil?
-    collection = JSON.parse(collection)
+          kb = get_knowledge_base name
+          matches = collection.keys.inject({}){|acc,type|
+            entities = collection[type]
+            entities.each do |entity|
+              _matches_h = kb.neighbours(database, entity)
+              _matches_h.each do |key, _matches|
+                target_type = _matches.target_entity_type
+
+                _matches = acc[target_type].concat _matches if acc[target_type] and acc[target_type].any?
+
+                acc.merge!({ target_type => _matches }) if _matches and _matches.any?
+              end
+            end
+            acc
+          }
+
+          @format ||= :json
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Parents: #{ [name, database] }")
+          when :json
+            content_type :json
+            _matches = {}
+            matches.each{|type,list|
+              _matches[type] = list.target.uniq.sort
+            }
+            halt 200, _matches.to_json
+          else
+            content_type :text
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.target * "\n"
+          end
+        end
 
-    kb = get_knowledge_base name
-    matches = collection.keys.inject({}){|acc,type|
-      entities = collection[type]
-      entities.each do |entity|
-        _matches_h = kb.neighbours(database, entity)
-        _matches_h.each do |key, _matches|
-          target_type = _matches.target_entity_type
+        get '/knowledge_base/:name/:database/subset' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          source = consume_parameter :source
+          target = consume_parameter :target
 
-          _matches = acc[target_type].concat _matches if acc[target_type] and acc[target_type].any?
+          source = source == "all" ? :all : source.split(@array_separator) if source
+          target = target == "all" ? :all : target.split(@array_separator) if target
+          entities = { :source => source, :target => target }
 
-          acc.merge!({ target_type => _matches }) if _matches and _matches.any?
+          kb = get_knowledge_base name
+          subset = kb.subset(database, entities)
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            halt 200, subset.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/subset', {:subset => subset}, "Subset: #{ [name, database] }")
+          when :json
+            content_type :json
+            halt 200, subset.source.to_json
+          else
+            content_type :text
+            halt 200, subset.source * "\n"
+          end
         end
-      end
-      acc
-    }
-
-    @format ||= :json
-    case @format
-    when :tsv
-      content_type "text/tab-separated-values"
-      matches = matches.sort_by{|k,list| list.length }.last.last
-      halt 200, matches.tsv.to_s
-    when :html
-      template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Parents: #{ [name, database] }")
-    when :json
-      content_type :json
-      _matches = {}
-      matches.each{|type,list|
-        _matches[type] = list.target.uniq.sort
-      }
-      halt 200, _matches.to_json
-    else
-      content_type :text
-      matches = matches.sort_by{|k,list| list.length }.last.last
-      halt 200, matches.target * "\n"
-    end
-  end
 
-  get '/knowledge_base/:name/:database/subset' do 
-    name = consume_parameter :name
-    database = consume_parameter :database
-    source = consume_parameter :source
-    target = consume_parameter :target
-
-    source = source == "all" ? :all : source.split(@array_separator) if source
-    target = target == "all" ? :all : target.split(@array_separator) if target
-    entities = { :source => source, :target => target }
-
-    kb = get_knowledge_base name
-    subset = kb.subset(database, entities)
-    case @format
-    when :tsv
-      content_type "text/tab-separated-values"
-      halt 200, subset.tsv.to_s
-    when :html
-      template_render('knowledge_base_partials/subset', {:subset => subset}, "Subset: #{ [name, database] }")
-    when :json
-      content_type :json
-      halt 200, subset.source.to_json
-    else
-      content_type :text
-      halt 200, subset.source * "\n"
-    end
-  end
+        #{{{ Info
 
-  #{{{ Info
+        get '/knowledge_base/info/:name/:database/:pair' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          pair = consume_parameter :pair
 
-  get '/knowledge_base/info/:name/:database/:pair' do 
-    name = consume_parameter :name
-    database = consume_parameter :database
-    pair = consume_parameter :pair
+          kb = get_knowledge_base name
+          index = kb.get_index(database)
 
-    kb = get_knowledge_base name
-    index = kb.get_index(database)
+          AssociationItem.setup(pair, kb, database, false)
+          template_render('knowledge_base_partials/association', {:pair => pair, :kb => kb, :index => index, :database => database}, "Association: #{ pair } #{[name, database] * ":"}", :cache_type => :async)
+        end
 
-    AssociationItem.setup(pair, kb, database, false)
-    template_render('knowledge_base_partials/association', {:pair => pair, :kb => kb, :index => index, :database => database}, "Association: #{ pair } #{[name, database] * ":"}", :cache_type => :async)
-  end
+        #{{{ Children
 
-  #{{{ Children
+        get '/knowledge_base/:name/:database/entity_children/:entity' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entity = consume_parameter :entity
 
-  get '/knowledge_base/:name/:database/entity_children/:entity' do
-    name = consume_parameter :name
-    database = consume_parameter :database
-    entity = consume_parameter :entity
+          kb = get_knowledge_base name
+          found = kb.identify database, entity
+          raise ParameterException, "Entity #{entity} was not found" unless found
 
-    kb = get_knowledge_base name
-    found = kb.identify database, entity
-    raise ParameterException, "Entity #{entity} was not found" unless found
+          list = kb.children(database, found).target_entity
 
-    list = kb.children(database, found).target_entity
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, prepare_entities_for_json(list).to_json
+          when :html
+          end
+        end
 
-    case @format
-    when :json
-      content_type "application/json"
-      halt 200, prepare_entities_for_json(list).to_json
-    when :html
-    end
-  end
+        # List children
+        post '/knowledge_base/:name/:database/entity_list_children/' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entities = consume_parameter :entities
 
-  # List children
-  post '/knowledge_base/:name/:database/entity_list_children/' do
-    name = consume_parameter :name
-    database = consume_parameter :database
-    entities = consume_parameter :entities
+          raise ParameterException, "No 'entities' provided" if entities.nil?
 
-    raise ParameterException, "No 'entities' provided" if entities.nil?
+          entities = entities.split("|")
 
-    entities = entities.split("|")
+          kb = get_knowledge_base name
 
-    kb = get_knowledge_base name
+          children = {}
+          entities.each do |entity|
+            found = kb.identify database, entity
+            next if found.nil?
+            children[entity] = kb.children(database, found).target_entity
+          end
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, prepare_entities_for_json(children).to_json
+          when :html
+          end
+        end
 
-    children = {}
-    entities.each do |entity|
-      found = kb.identify database, entity
-      next if found.nil?
-      children[entity] = kb.children(database, found).target_entity
-    end
-    case @format
-    when :json
-      content_type "application/json"
-      halt 200, prepare_entities_for_json(children).to_json
-    when :html
-    end
-  end
+        # Collection children
+        post '/knowledge_base/:name/:database/entity_collection_children' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entities = consume_parameter :entities
 
-  # Collection children
-  post '/knowledge_base/:name/:database/entity_collection_children' do
-    name = consume_parameter :name
-    database = consume_parameter :database
-    entities = consume_parameter :entities
+          raise ParameterException, "No 'entities' provided" if entities.nil?
 
-    raise ParameterException, "No 'entities' provided" if entities.nil?
+          entities = JSON.parse(entities)
 
-    entities = JSON.parse(entities)
+          kb = get_knowledge_base name
 
-    kb = get_knowledge_base name
+          entities.each do |type,list|
+            list.each do |entity|
+              found = kb.identify database, entity
+              next if found.nil?
+              targets = kb.children(database, found).target_entity
+              next if targets.nil? or targets.empty?
+              target_type = kb.target database
+              children[target_type] ||= []
+              children[target_type].concat targets
+            end
+          end
 
-    entities.each do |type,list|
-      list.each do |entity|
-        found = kb.identify database, entity
-        next if found.nil?
-        targets = kb.children(database, found).target_entity
-        next if targets.nil? or targets.empty?
-        target_type = kb.target database
-        children[target_type] ||= []
-        children[target_type].concat targets
-      end
-    end
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, prepare_entities_for_json(children).to_json
+          when :html
+          end
+        end
 
-    case @format
-    when :json
-      content_type "application/json"
-      halt 200, prepare_entities_for_json(children).to_json
-    when :html
-    end
-  end
+        #{{{ Neighbours
 
-  #{{{ Neighbours
+        get '/knowledge_base/:name/:database/entity_neighbours/:entity' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entity = consume_parameter :entity
 
-  get '/knowledge_base/:name/:database/entity_neighbours/:entity' do
-    name = consume_parameter :name
-    database = consume_parameter :database
-    entity = consume_parameter :entity
+          kb = get_knowledge_base name
+          found = kb.identify database, entity
+          raise ParameterException, "Entity #{entity} was not found" unless found
 
-    kb = get_knowledge_base name
-    found = kb.identify database, entity
-    raise ParameterException, "Entity #{entity} was not found" unless found
+          list = kb.neighbours(database, found).values.select{|list| list and list.any?}.first
+          list = list.target_entity if list.respond_to? :target_entity
+          list ||= []
 
-    list = kb.neighbours(database, found).values.select{|list| list and list.any?}.first
-    list = list.target_entity if list.respond_to? :target_entity
-    list ||= []
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, prepare_entities_for_json(list).to_json
+          when :html
+          end
+        end
 
-    case @format
-    when :json
-      content_type "application/json"
-      halt 200, prepare_entities_for_json(list).to_json
-    when :html
-    end
-  end
+        post '/knowledge_base/:name/:database/entity_list_neighbours/' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entities = consume_parameter :entities
 
-  post '/knowledge_base/:name/:database/entity_list_neighbours/' do
-    name = consume_parameter :name
-    database = consume_parameter :database
-    entities = consume_parameter :entities
+          raise ParameterException, "No 'entities' provided" if entities.nil?
 
-    raise ParameterException, "No 'entities' provided" if entities.nil?
+          entities = entities.split("|")
 
-    entities = entities.split("|")
+          kb = get_knowledge_base name
 
-    kb = get_knowledge_base name
+          children = {}
+          entities.each do |entity|
+            found = kb.identify database, entity
+            next if found.nil?
+            matches = kb.neighbours(database, found).values.select{|list| list and list.any?}.first
+            next if matches.nil? or matches.empty?
+            children[entity] = matches.target_entity
+          end
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, prepare_entities_for_json(children).to_json
+          when :html
+          end
+        end
 
-    children = {}
-    entities.each do |entity|
-      found = kb.identify database, entity
-      next if found.nil?
-      matches = kb.neighbours(database, found).values.select{|list| list and list.any?}.first
-      next if matches.nil? or matches.empty?
-      children[entity] = matches.target_entity
-    end
-    case @format
-    when :json
-      content_type "application/json"
-      halt 200, prepare_entities_for_json(children).to_json
-    when :html
-    end
-  end
+        post '/knowledge_base/:name/:database/entity_collection_neighbours' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entities = consume_parameter :entities
 
-  post '/knowledge_base/:name/:database/entity_collection_neighbours' do
-    name = consume_parameter :name
-    database = consume_parameter :database
-    entities = consume_parameter :entities
+          raise ParameterException, "No 'entities' provided" if entities.nil?
 
-    raise ParameterException, "No 'entities' provided" if entities.nil?
+          entities = JSON.parse(entities)
 
-    entities = JSON.parse(entities)
+          kb = get_knowledge_base name
 
-    kb = get_knowledge_base name
+          neighbours = {}
+          entities.each do |type,list|
+            list.each do |entity|
+
+              found = kb.identify_source database, entity
+              if found.nil?
+                reverse = true
+                found = kb.identify_target database, entity
+              else
+                reverse = false
+              end
+              next if found.nil?
+
+              matches = kb.neighbours(database, found)[reverse ? :parents : :children]
+              next if matches.nil? or matches.empty?
+              targets = matches.target
+
+              entity_type = reverse ? kb.source_type(database) : kb.target_type(database)
+              neighbours[entity_type] ||= []
+              neighbours[entity_type].concat targets
+            end
+          end
 
-    neighbours = {}
-    entities.each do |type,list|
-      list.each do |entity|
+          neighbours.each{|type, list| list.uniq!}
 
-        found = kb.identify_source database, entity
-        if found.nil?
-          reverse = true
-          found = kb.identify_target database, entity
-        else
-          reverse = false
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, prepare_entities_for_json(neighbours).to_json
+          when :html
+          end
         end
-        next if found.nil?
 
-        matches = kb.neighbours(database, found)[reverse ? :parents : :children]
-        next if matches.nil? or matches.empty?
-        targets = matches.target
+        get '/kb/:name/:database/children/:entity' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entity = consume_parameter :entity
 
-        entity_type = reverse ? kb.source_type(database) : kb.target_type(database)
-        neighbours[entity_type] ||= []
-        neighbours[entity_type].concat targets
-      end
-    end
+          kb = get_knowledge_base name
+          found = kb.identify database, entity
+          raise ParameterException, "Entity #{entity} was not found" unless found
 
-    neighbours.each{|type, list| list.uniq!}
+          iii kb.children(database, found)
+          list = kb.children(database, found).target_entity
 
-    case @format
-    when :json
-      content_type "application/json"
-      halt 200, prepare_entities_for_json(neighbours).to_json
-    when :html
-    end
-  end
+          content_type "application/json"
+          halt 200, serialize_entities(list).to_json
+        end
+
+        get '/kb/:name/:database/parents/:entity' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entity = consume_parameter :entity
+
+          kb = get_knowledge_base name
+          found = kb.identify database, entity
+          raise ParameterException, "Entity #{entity} was not found" unless found
+
+          iii kb.parents(database, found)
+          list = kb.parents(database, found).target_entity
+
+          content_type "application/json"
+          halt 200, serialize_entities(list).to_json
+        end
       end
     end
   end