rbbt-rest 1.1.4 → 1.1.5

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

@@ -30,7 +30,11 @@ module Sinatra
     def self.registered(app)
       app.helpers RbbtAuth::Helpers
 
-      app.set :users, Rbbt.etc.web_users.yaml
+      if Rbbt.etc.web_users.exists?
+        app.set :users, Rbbt.etc.web_users.yaml
+      else
+        app.set :users, {}
+      end
 
       app.get '/login' do
         "<form class='login' method='POST' action='/login'>" +

data/lib/rbbt/rest/entity.rb

@@ -11,16 +11,20 @@ require 'rbbt/rest/entity/locate'
 require 'rbbt/rest/entity/helpers'
 require 'rbbt/rest/entity/render'
 require 'rbbt/rest/entity/list'
+require 'rbbt/rest/entity/map'
 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/entity_map_card'
 require 'rbbt/rest/entity/action_card'
 require 'rbbt/rest/entity/list_container'
 require 'rbbt/rest/entity/action_controller'
 
+require 'rbbt/statistics/rank_product'
+
 
 module Sinatra
   module RbbtRESTEntity
@@ -30,6 +34,7 @@ module Sinatra
 
         set :favourites_dir, Rbbt.var.find.sinatra.favourites
         set :favourite_lists_dir, Rbbt.var.find.sinatra.favourite_lists
+        set :favourite_maps_dir, Rbbt.var.find.sinatra.favourite_maps
         set :finder, nil
 
         get /^\/entity.*/ do
@@ -37,6 +42,42 @@ module Sinatra
           pass
         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
+
+
         #{{{ Entities
 
         get '/entity/:entity_type/:entity' do
@@ -100,6 +141,8 @@ module Sinatra
 
           list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
 
+          raise "List not found" if list.nil?
+
           case @format
           when :raw, :literal
             content_type "text/tab-separated-values"
@@ -111,30 +154,20 @@ module Sinatra
 
             raise "List file not found: #{ list_id }"
           when :json
-            list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
             list_info = {:entities => list, :info => list.info}
             halt 200, list_info.to_json
           when :info
-            list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
             halt 200, list.info.to_json
           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
@@ -154,6 +187,8 @@ module Sinatra
         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)
 
@@ -179,6 +214,234 @@ module Sinatra
           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 = TSVWorkflow.job(:change_id, "Map #{ map_id }", :format => "Associated Gene Name", :tsv => TSV.open(file)).exec
+            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 = TSVWorkflow.job(:change_id, "Map #{ map_id }", :format => "Ensembl Gene ID", :tsv => TSV.open(file)).exec
+            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
+              (1 - value.to_f) / value.to_f
+            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)
+            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"
+            halt 200, TSV.open(file).to_json
+          else
+            map = Entity::Map.load_map(entity_type.split(":").first, column, map_id, user)
+            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])
+
+          map = Entity::Map.load_map(entity_type.split(":").first, 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
+          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)
+
+          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
+          tsv2 =  TSV.open(file2)
+
+          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
+
+        #{{{{{{{{{{{{{{
+        #{{{ FAVOURITES
+        #{{{{{{{{{{{{{{
+
+
         #{{{ Favourite entities
 
         post '/add_favourite_entity/:entity_type/:entity' do
@@ -232,6 +495,8 @@ module Sinatra
           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)
@@ -243,6 +508,7 @@ module Sinatra
           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)
@@ -259,109 +525,48 @@ module Sinatra
           favs.to_json
         end
 
-        #{{{ Finder
-
-
-        get '/find' do
-          halt 200 if params[:term].nil? or params[:term].empty?
+        #{{{ 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
 
-          term = params[:term]
-          sorted_results = finder_find(term)
+          map = Entity::REST.restore_element(map)
 
-          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
+          entity_type = Entity::REST.restore_element(entity_type).split(":").first
+          column = Entity::REST.restore_element(column)
 
-        post '/find' do
-          term = consume_parameter :term 
-          if term =~ /(.*) \[(.*)\]$/
-            term = $1
-            namespace, format = $2.split(":")
-            format, namespace = namespace, nil if format.nil?
+          add_favourite_entity_map(entity_type, column, map)
 
-            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
+          halt 200
         end
 
-        #{{{ List Management
-        
-        get '/entity_list/intersect/:entity_type/:list_id' do
+        post '/remove_favourite_entity_map/:entity_type/:column/:map' do
           entity_type = consume_parameter :entity_type
-          list_id = consume_parameter :list_id
-          other_list_id = consume_parameter :other_list_id
+          column = consume_parameter :column
+          map = consume_parameter :map
 
-          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)
+          map = Entity::REST.restore_element(map)
 
-          new_list = list.subset(other_list)
-          new_list_id = [list_id, other_list_id] * " ^ "
+          entity_type = Entity::REST.restore_element(entity_type).split(":").first
+          column = Entity::REST.restore_element(column)
 
-          Entity::List.save_list(type, new_list_id, new_list, user) 
+          remove_favourite_entity_map(entity_type, column, map)
 
-          redirect to(Entity::REST.entity_list_url(new_list_id, type))
+          halt 200
         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] * " - "
+        get '/favourite_entity_maps' do
+          content_type "application/json"
 
-          Entity::List.save_list(type, new_list_id, new_list, user) 
+          favs = favourite_entity_maps
 
-          redirect to(Entity::REST.entity_list_url(new_list_id, type))
+          favs.to_json
         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