Module: Sinatra::RbbtRESTEntity

Defined in:

lib/rbbt/rest/entity.rb

Class Method Summary

• .registered(base) ⇒ Object

Class Method Details

.registered(base) ⇒ Object

# File 'lib/rbbt/rest/entity.rb', line 32

def self.registered(base)
  base.module_eval do
    helpers EntityRESTHelpers


    get /\/entity.*/ do
      @cache_type = :asynchronous if @cache_type.nil?
      pass
    end

    #{{{ Finder

    get '/find' do
      raise "No finder defined" unless settings.respond_to? :finder and not settings.finder.nil?
      halt 200 if params[:term].nil? or params[:term].empty?
      term = params[:term]
      if request.xhr?
        sorted_results = finder_find(term)
        content_type "application/json" 
        halt 200, sorted_results.to_json
      else
        url = find_entity_url(term)
        redirect to(url)
      end
    end

    post '/find' do
      term = consume_parameter :term 
      url = find_entity_url(term)
      redirect to(url)
    end



    #{{{ Entities

    get '/entity/:entity_type/:entity' do
      entity_type = consume_parameter :entity_type
      entity = consume_parameter :entity

      entity = Entity::REST.restore_element(entity)

      entity_type = Entity::REST.restore_element(entity_type)

      entity = setup_entity(entity_type, entity, @clean_params)

      @entity = entity

      entity_render(entity, @clean_params)
    end

    get '/entity_action/:entity_type/:action/:entity' do
      entity_type = consume_parameter :entity_type
      entity = consume_parameter :entity
      action = consume_parameter :action

      entity = Entity::REST.restore_element(entity)

      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 :json
        content_type "application/json"
        halt 200, list_json(list)
      when :info
        content_type "application/json"
        halt 200, list.info.to_json
      when :list
        content_type "text/plain"
        halt 200, list * "\n"
      when :name
        name = list.name
        if name.respond_to? :list_link
          a = name.list_link :length, list_id.sub(/ \(format:.*?\)|$/, " (format: Name)"), :ensembl => false
          redirect to(a.match(/href=(["'])(.*?)\1/)[2])
        else
          content_type "text/plain"
          halt 200, name * "\n"
        end
      when :ensembl
        ensembl = list.ensembl
        a = ensembl.list_link :length, list_id.sub(/ \(format:.*?\)|$/, " (format: Ensembl)")
        redirect to(a.match(/href=(["'])(.*?)\1/)[2])
      else
        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

      list_id = list_id.gsub("'", '"')

      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

    #{{{ 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] * " ^ "
      new_list_id = [Misc.digest(list_id), Misc.digest(other_list_id)] * " ^ " if new_list_id.length > 200

      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] * " - "
      new_list_id = [Misc.digest(list_id), Misc.digest(other_list_id)] * " ~ " if new_list_id.length > 200

      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 "
      new_list_id = [Misc.digest(list_id), Misc.digest(other_list_id)] * " PLUS " if new_list_id.length > 200

      Entity::List.save_list(type, new_list_id, new_list, user) 

      redirect to(Entity::REST.entity_list_url(new_list_id, type))
    end

    #{{{ Entity maps
   
    get '/entity_map/:entity_type/:column/:map_id' do
      entity_type = consume_parameter :entity_type
      map_id = consume_parameter :map_id
      column = consume_parameter :column

      entity_type = Entity::REST.restore_element(entity_type)
      column = Entity::REST.restore_element(column)
      map_id = Entity::REST.restore_element(map_id)

      map = Entity::Map.load_map(entity_type.split(":").first, column, map_id, user)

      case @format
      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 = 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))
      when :ensembl
        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 = TSV.open(file).change_key "Ensembl Gene ID"
        new_id = map_id << " [Ensembl]"
        Entity::Map.save_map(entity_type, column, new_id, new, user)
        redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
      when :pvalue_score
        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
        tsv =  TSV.open(file)
        tsv.process tsv.fields.first do |value|
          value = value.flatten.first if Array === value
          - Math.log(value.to_f.abs) * (value.to_f >= 0 ? 1 : -1)
        end
        tsv.fields = [tsv.fields.first + " score"]
        tsv.type = :single
        tsv.cast = :to_f
        new_id = map_id << " [Pvalue score]"
        column = 'Pvalue Score'
        Entity::Map.save_map(entity_type, column, new_id, tsv, user)
        redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
      when :ranks
        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
        tsv =  TSV.open(file, :cast => :to_f)
        new = tsv.ranks_for(tsv.fields.first)
        new_id = map_id << " [Ranks]"
        column = 'Ranks'
        Entity::Map.save_map(entity_type, column, new_id, new, user)
        redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
      when :invert_ranks
        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
        tsv =  TSV.open(file)
        size = tsv.size
        tsv.process "Rank" do |v|
          if Array === v
            [(size - v.first.to_i).to_s]
          else
            (size - v.to_i).to_s
          end
        end
        new_id = map_id.dup
        column = 'Ranks'
        Entity::Map.save_map(entity_type, column, new_id, tsv, user)
        redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
      when :raw, :literal
        content_type "text/tab-separated-values"
        user_file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
        send_file user_file if File.exists? user_file

        global_file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil)
        send_file global_file if File.exists? global_file

        raise "Map file not found: #{ map_id }"
      when :json
        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

        content_type "application/json"
        tsv = TSV.open(file)
        halt 200, tsv.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

    get '/entity_map_action/:entity_type/:column/:action/:map_id' do
      action = consume_parameter :action

      entity_type = Entity::REST.restore_element(consume_parameter :entity_type)
      column = Entity::REST.restore_element(consume_parameter :column)
      map_id = Entity::REST.restore_element(consume_parameter :map_id)

      map = Entity::Map.load_map(entity_type.split(":").first, column, map_id, user)

      entity_map_action_render(map, action, map_id, @clean_params)
    end

 
    get '/entity_map/rename/:entity_type/:column/:map_id' do
      new_id = params[:new_name]

      entity_type = Entity::REST.restore_element(params[:entity_type])
      column = Entity::REST.restore_element(params[:column])
      map_id = Entity::REST.restore_element(params[:map_id])

      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)

      redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
    end

    get '/entity_map/rank_products' do
      map1 = consume_parameter :map1
      map2 = consume_parameter :map2

      map1 = Entity::REST.restore_element(map1)
      map2 = Entity::REST.restore_element(map2)

      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
      raise "Map not found: #{ map1 }" unless File.exists? file1
      tsv1 =  TSV.open(file1, :cast => :to_f) 

      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, :cast => :to_f)

      tsv1 = tsv1.select :key => tsv2.keys
      tsv1.attach tsv2, :fields => tsv2.fields

      new = TSV.setup(tsv1.rank_product(tsv1.fields), :key_field => tsv1.key_field, :fields => ["Log rank-product"], :type => :single, :cast => :to_f)
      new.entity_options = tsv1.entity_options
      new.namespace = tsv1.namespace

      new_id = "Rank products of #{ map1 } ~ #{ map2 }"
      if new_id.length > 200
        new_id = "Rank products of #{ Misc.digest(map1) } ~ #{ Misc.digest(map2) }"
      end

      column = 'Log rank-product'
      Entity::Map.save_map(entity_type, column, new_id, new, user)
      redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
    end

    #{{{{{{{{{{{{{{
    #{{{ PROPERTIES
    #{{{{{{{{{{{{{{

    get '/entity_property/:property/:entity_type/:entity' do
      entity_type = consume_parameter :entity_type
      entity = consume_parameter :entity
      property = consume_parameter :property
      args = consume_parameter :args

      if args.nil?
        args = []  
      else
        args = begin
                 JSON.parse(args)
               rescue
                 args
               end
      end

      case args
      when Hash
        args = [args] 
      when String
        args = args.split(/[,\|]/)
      end

      entity_type = Entity::REST.restore_element(entity_type)

      entity = setup_entity(entity_type, entity, @clean_params)

      begin
        res = entity.send(property,*args)
      rescue
        if entity.respond_to?(:format) and  entity.base_type.respond_to?(:default_format) and entity.format != entity.base_type.default_format
          entity = entity.to(:default)
          Log.warn "Error computing property #{property} for #{entity}. Automatically changing entity format to default"
          retry
        else
          raise $!
        end
      end

      case res
      when String
        content_type "application/json"
        halt 200, '"' + res + '"'
      when Fixnum
        content_type :text
        halt 200, res.to_s
      else
        content_type "application/json"
        halt 200, res.to_json
      end
    end

    get '/entity_list_property/:property/:entity_type/:list_id' do
      entity_type = consume_parameter :entity_type
      list_id = consume_parameter :list_id
      property = consume_parameter :property

      args = consume_parameter :args

      if args.nil?
        args = []  
      else
        args = begin
                 JSON.parse(args)
               rescue
                 args
               end
      end

      case args
      when Hash
        args = [args] 
      when String
        args = args.split(/[,\|]/)
      end


      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)

      content_type "application/json"
      halt 200, list.send(property, *args).to_json
    end

    post '/entity_list_property/:property/:entity_type' do
      entity_type = consume_parameter :entity_type
      property = consume_parameter :property
      list = consume_parameter :list
      info = consume_parameter :info
      args = consume_parameter :args

      info = (info.nil? or info.empty?) ? {} : JSON.parse(info)
      entity_type = Entity::REST.restore_element(entity_type)
      list = Misc.prepare_entity(list.split(/[,|]/), entity_type, info)
      list.extend AnnotatedArray

      args = (args.nil? or args.empty?) ? nil : begin JSON.parse(args) rescue args end
      case args
      when Hash
        args = [args] 
      when String
        args = args.split(/[,\|]/)
      end

      begin
        res = list.send(property,*args)
      rescue
        Log.exception $!
        if list.respond_to?(:format) and list.base_type.respond_to?(:default_format) and list.format != list.base_type.default_format
          list = list.to(:default)
          Log.warn "Error computing property #{property} for list. Automatically changing list format to default"
          retry
        else
          raise $!
        end
      end

      case res
      when String
        content_type "application/json"
        halt 200, '"' + res + '"'
      when Fixnum
        content_type :text
        halt 200, res.to_s
      else
        content_type "application/json"
        halt 200, res.to_json
      end
    end



    #{{{{{{{{{{{{{{
    #{{{ FAVOURITES
    #{{{{{{{{{{{{{{


    #{{{ 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| 
          next unless entity.respond_to? :link
          info = entity.info
          info.delete :annotation_types
          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
      }

      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

      list = Entity::REST.restore_element(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

      list = Entity::REST.restore_element(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

    #{{{ Favourite entity maps
 
    post '/add_favourite_entity_map/:entity_type/:column/:map' do
      entity_type = consume_parameter :entity_type
      column = consume_parameter :column
      map = consume_parameter :map

      map = Entity::REST.restore_element(map)

      entity_type = Entity::REST.restore_element(entity_type).split(":").first
      column = Entity::REST.restore_element(column)

      add_favourite_entity_map(entity_type, column, map)

      halt 200
    end

    post '/remove_favourite_entity_map/:entity_type/:column/:map' do
      entity_type = consume_parameter :entity_type
      column = consume_parameter :column
      map = consume_parameter :map

      map = Entity::REST.restore_element(map)

      entity_type = Entity::REST.restore_element(entity_type).split(":").first
      column = Entity::REST.restore_element(column)

      remove_favourite_entity_map(entity_type, column, map)

      halt 200
    end


    get '/favourite_entity_maps' do
      content_type "application/json"

      favs = favourite_entity_maps

      favs.to_json
    end

 
  end
end