rbbt-rest 1.1.0

data/lib/rbbt/rest/entity.rb

@@ -0,0 +1,362 @@
+require 'rbbt'
+require 'rbbt/workflow'
+require 'sinatra/base'
+require 'json'
+
+require 'rbbt/rest/common/locate'
+require 'rbbt/rest/common/misc'
+require 'rbbt/rest/common/users'
+
+require 'rbbt/rest/entity/locate'
+require 'rbbt/rest/entity/helpers'
+require 'rbbt/rest/entity/render'
+require 'rbbt/rest/entity/list'
+require 'rbbt/rest/entity/rest'
+require 'rbbt/rest/entity/favourites'
+require 'rbbt/rest/entity/finder'
+
+require 'rbbt/rest/entity/entity_card'
+require 'rbbt/rest/entity/entity_list_card'
+require 'rbbt/rest/entity/action_card'
+require 'rbbt/rest/entity/list_container'
+require 'rbbt/rest/entity/action_controller'
+
+
+module Sinatra
+  module RbbtRESTEntity
+    def self.registered(base)
+      base.module_eval do
+        helpers EntityRESTHelpers
+
+        set :favourites_dir, Rbbt.var.find.sinatra.favourites
+        set :favourite_lists_dir, Rbbt.var.find.sinatra.favourite_lists
+        set :finder, nil
+
+        get /^\/entity.*/ do
+          @cache_type = :asynchronous if @cache_type.nil?
+          pass
+        end
+
+        #{{{ Entities
+
+        get '/entity/:entity_type/:entity' do
+          entity_type = consume_parameter :entity_type
+          entity = consume_parameter :entity
+
+          entity_type = Entity::REST.restore_element(entity_type)
+
+          entity = setup_entity(entity_type, entity, @clean_params)
+
+          @entity = entity
+
+          entity_render(entity)
+        end
+
+        get '/entity_action/:entity_type/:action/:entity' do
+          entity_type = consume_parameter :entity_type
+          entity = consume_parameter :entity
+          action = consume_parameter :action
+
+          entity_type = Entity::REST.restore_element(entity_type)
+
+          entity = setup_entity(entity_type, entity, @clean_params)
+
+          @entity = entity
+
+          entity_action_render(entity, action, @clean_params)
+        end
+
+        #{{{ Entity lists
+
+        get '/entity_list/:entity_type/new/' do
+          entity_type = consume_parameter :entity_type
+
+          entity_type = Entity::REST.restore_element(entity_type)
+
+          mod = Entity.formats[entity_type.split(":").first]
+          list = mod.setup([])
+
+          entity_list_action_render(list, 'new', "New #{mod} list", @clean_params.merge(:entity_type => entity_type))
+        end
+ 
+        get '/entity_list/:entity_type/edit/:list_id' do
+          entity_type = consume_parameter :entity_type
+          list_id = consume_parameter :list_id
+
+          entity_type = Entity::REST.restore_element(entity_type)
+          list_id = Entity::REST.restore_element(list_id)
+
+          list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
+
+          entity_list_action_render(list, 'edit', list_id, @clean_params)
+        end
+               
+        get '/entity_list/:entity_type/:list_id' do
+          entity_type = consume_parameter :entity_type
+          list_id = consume_parameter :list_id
+
+          entity_type = Entity::REST.restore_element(entity_type)
+          list_id = Entity::REST.restore_element(list_id)
+
+          list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
+
+          case @format
+          when :raw, :literal
+            content_type "text/tab-separated-values"
+            user_file = Entity::List.list_file(entity_type.split(":").first, list_id, user)
+            send_file user_file if File.exists? user_file
+
+            global_file = Entity::List.list_file(entity_type.split(":").first, list_id, nil)
+            send_file global_file if File.exists? global_file
+
+            raise "List file not found: #{ list_id }"
+          when :list
+            list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
+            
+            content_type "text/plain"
+            halt 200, list * "\n"
+          when :name
+            list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
+            
+            content_type "text/plain"
+           
+            halt 200, list.name * "\n"
+          when :ensembl
+            list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
+            
+            content_type "text/plain"
+            halt 200, list.ensembl * "\n"
+          else
+            list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
+            entity_list_render(list, list_id)
+          end
+        end
+
+        get '/entity_list_action/:entity_type/:action/:list_id' do
+          entity_type = consume_parameter :entity_type
+          list_id = consume_parameter :list_id
+          action = consume_parameter :action
+
+          entity_type = Entity::REST.restore_element(entity_type)
+          list_id = Entity::REST.restore_element(list_id)
+          list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
+
+          entity_list_action_render(list, action, list_id, @clean_params)
+        end
+
+        post '/entity_list/:entity_type/:list_id' do
+          list_id = consume_parameter :list_id
+
+          entity_type = consume_parameter :entity_type
+          entity_type = Entity::REST.restore_element(entity_type)
+
+          type, format = entity_type.split(":")
+
+          entities = consume_parameter :entities
+          entity_file = consume_parameter :entities__param_file
+
+          entities = fix_input(:array, entities, entity_file)
+
+          annotations = consume_parameter :annotations
+          annotations = JSON.parse(annotations)
+          
+          annotations[:format] = format if format
+
+          annotations[:annotation_types] ||= [type]
+
+          mod = Kernel.const_get(type)
+          list = mod.setup(entities.reject{|e| e.empty?}, annotations)
+
+          Entity::List.save_list(type, list_id, list, user)
+
+          redirect to(Entity::REST.entity_list_url(list_id, type))
+        end
+
+        #{{{ Favourite entities
+
+        post '/add_favourite_entity/:entity_type/:entity' do
+          entity_type = consume_parameter :entity_type
+          entity = consume_parameter :entity
+
+          entity_type = Entity::REST.restore_element(entity_type)
+
+          entity = setup_entity(entity_type, entity, @clean_params)
+
+          add_favourite_entity(entity)
+
+          halt 200
+        end
+
+        post '/remove_favourite_entity/:entity_type/:entity' do
+          entity_type = consume_parameter :entity_type
+          entity = consume_parameter :entity
+
+          entity_type = Entity::REST.restore_element(entity_type)
+
+          entity = setup_entity(entity_type, entity, @clean_params)
+
+          remove_favourite_entity(entity)
+
+          halt 200
+        end
+
+
+        get '/favourite_entities' do
+          content_type "application/json"
+
+          favs = {}
+
+          favourite_entities.each{|type, list|
+            type_favs = {}
+            list.each do |entity| 
+              info = entity.info
+              info.delete :annotation_types
+              type_favs[entity] = {:info => info, :link => entity.link} 
+            end
+            favs[type] = type_favs
+          }
+
+          favs.to_json
+        end
+ 
+        #{{{ Favourite entity lists
+
+        post '/add_favourite_entity_list/:entity_type/:list' do
+          entity_type = consume_parameter :entity_type
+          list = consume_parameter :list
+
+          entity_type = Entity::REST.restore_element(entity_type).split(":").first
+
+          add_favourite_entity_list(entity_type, list)
+
+          halt 200
+        end
+
+        post '/remove_favourite_entity_list/:entity_type/:list' do
+          entity_type = consume_parameter :entity_type
+          list = consume_parameter :list
+
+          entity_type = Entity::REST.restore_element(entity_type).split(":").first
+
+          remove_favourite_entity_list(entity_type, list)
+
+          halt 200
+        end
+
+
+        get '/favourite_entity_lists' do
+          content_type "application/json"
+
+          favs = favourite_entity_lists
+
+          favs.to_json
+        end
+
+        #{{{ Finder
+
+
+        get '/find' do
+          halt 200 if params[:term].nil? or params[:term].empty?
+
+          term = params[:term]
+          sorted_results = finder_find(term)
+
+          raise "No finder defined" unless settings.respond_to? :finder and not settings.finder.nil?
+          if request.xhr?
+            content_type "application/json" 
+            halt 200, sorted_results.to_json
+          else
+            i = sorted_results.first
+            raise "Term not recognized: #{ term }" if i.nil?
+            redirect to(Entity::REST.entity_url(i[:code], i[:format], i[:namespace]))
+          end
+        end
+
+        post '/find' do
+          term = consume_parameter :term 
+          if term =~ /(.*) \[(.*)\]$/
+            term = $1
+            namespace, format = $2.split(":")
+            format, namespace = namespace, nil if format.nil?
+
+            redirect to(Entity::REST.entity_url(term, format, :organism => namespace))
+          else
+            sorted_results = finder_find(term)
+            i = sorted_results.first
+            halt 404, "Term not recognized: #{ term }" if i.nil?
+            redirect to(Entity::REST.entity_url(i[:code], i[:format], :organism => i[:namespace]))
+          end
+        end
+
+        #{{{ List Management
+        
+        get '/entity_list/intersect/:entity_type/:list_id' do
+          entity_type = consume_parameter :entity_type
+          list_id = consume_parameter :list_id
+          other_list_id = consume_parameter :other_list_id
+
+          entity_type = Entity::REST.restore_element(entity_type)
+          type = entity_type.split(":").first
+
+          list_id = Entity::REST.restore_element(list_id)
+          list = Entity::List.load_list(type, list_id, user)
+
+          other_list_id = Entity::REST.restore_element(other_list_id)
+          other_list = Entity::List.load_list(type, other_list_id, user)
+
+          new_list = list.subset(other_list)
+          new_list_id = [list_id, other_list_id] * " ^ "
+
+          Entity::List.save_list(type, new_list_id, new_list, user) 
+
+          redirect to(Entity::REST.entity_list_url(new_list_id, type))
+        end
+ 
+        get '/entity_list/remove/:entity_type/:list_id' do
+          entity_type = consume_parameter :entity_type
+          list_id = consume_parameter :list_id
+          other_list_id = consume_parameter :other_list_id
+
+          entity_type = Entity::REST.restore_element(entity_type)
+          type = entity_type.split(":").first
+
+          list_id = Entity::REST.restore_element(list_id)
+          list = Entity::List.load_list(type, list_id, user)
+
+          other_list_id = Entity::REST.restore_element(other_list_id)
+          other_list = Entity::List.load_list(type, other_list_id, user)
+
+          new_list = list.remove(other_list)
+          new_list_id = [list_id, other_list_id] * " - "
+
+          Entity::List.save_list(type, new_list_id, new_list, user) 
+
+          redirect to(Entity::REST.entity_list_url(new_list_id, type))
+        end
+ 
+        get '/entity_list/add/:entity_type/:list_id' do
+          entity_type = consume_parameter :entity_type
+          list_id = consume_parameter :list_id
+          other_list_id = consume_parameter :other_list_id
+
+          entity_type = Entity::REST.restore_element(entity_type)
+          type = entity_type.split(":").first
+
+          list_id = Entity::REST.restore_element(list_id)
+          list = Entity::List.load_list(type, list_id, user)
+
+          other_list_id = Entity::REST.restore_element(other_list_id)
+          other_list = Entity::List.load_list(type, other_list_id, user)
+
+          new_list = list.concat(other_list)
+          new_list_id = [list_id, other_list_id] * " PLUS "
+
+          Entity::List.save_list(type, new_list_id, new_list, user) 
+
+          redirect to(Entity::REST.entity_list_url(new_list_id, type))
+        end
+      end
+    end
+  end
+end
+

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

@@ -0,0 +1,22 @@
+class ActionCard
+
+  attr_accessor :action_parameters, :requires
+  def initialize(&block)
+    @action_parameters = block
+    @requires = []
+  end
+
+  def require(*inputs, &block)
+    if block_given?
+      @requires << [inputs, block]
+    else
+      @requires.concat inputs
+    end
+  end
+end
+
+module EntityRESTHelpers
+  def action_card_render(card, &block)
+    partial_render('entity_partials/action_card', :card => card, :block => block)
+  end
+end

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

@@ -0,0 +1,38 @@
+class ActionController
+  attr_accessor :entity, :id
+  attr_accessor :actions
+
+  def initialize(entity, id = nil)
+    @entity, @id = entity, id
+    @actions = []
+  end
+
+  def add(action, text = nil, resource = nil, params = {})
+    text = action if text.nil?
+    resource = action.respond_to?(:resource) ? action.resource : nil
+    resource ||= "Rbbt"
+    @actions << [action, text, resource, params]
+  end
+
+end
+
+module EntityRESTHelpers
+  def default_action_controller(entity, list_id = nil)
+    action_controller = ActionController.new(entity, list_id)
+
+    if Array === entity
+      find_all_entity_list_action_templates(entity, true).each do |action|
+        action_controller.add action, Misc.humanize(action, :format => :sentence), :reuse => true
+      end
+    else
+      find_all_entity_action_templates(entity, true).each do |action|
+        action_controller.add action, Misc.humanize(action, :format => :sentence)
+      end
+    end
+    action_controller
+  end
+
+  def action_controller_render(controller)
+    partial_render('entity_partials/action_controller', :controller => controller)
+  end
+end

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

@@ -0,0 +1,26 @@
+class EntityCard
+
+  attr_accessor :entity
+  attr_accessor :name, :long_name, :description, :meta
+  attr_accessor :list_container, :action_controller
+
+  def initialize(entity)
+    @entity = entity
+  end
+
+  %w(name long_name description meta).each do |method|
+    self.send(:define_method, method.to_sym) do |&block|
+      if block
+        instance_variable_set("@#{method}", block)
+      else
+        instance_variable_get("@#{method}")
+      end
+    end
+  end
+end
+
+module EntityRESTHelpers
+  def entity_card_render(card)
+    partial_render('entity_partials/entity_card', :card => card)
+  end
+end