rbbt-rest 1.1.5 → 1.2.0

data/lib/rbbt/rest/helpers.rb

@@ -40,5 +40,12 @@ module Sinatra
       end
       bed
     end
+
+    def format_name(name)
+      parts = name.split("_")
+      hash = parts.pop
+      clean_name = parts * "_"
+      "<span class='name' jobname='#{ name }'>#{ clean_name }</span><span class='hash'>#{ hash }</span>"
+    end
   end
 end

data/lib/rbbt/rest/knowledge_base.rb

@@ -0,0 +1,338 @@
+require 'rbbt'
+require 'rbbt/workflow'
+require 'sinatra/base'
+
+require 'rbbt/knowledge_base'
+require 'rbbt/rest/knowledge_base/helpers'
+
+module Sinatra
+  module RbbtRESTKnowledgeBase
+    def self.registered(base)
+      base.module_eval do
+        helpers KnowledgeBaseRESTHelpers
+
+        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
+
+          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
+
+        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?
+
+          entities = entities.split("|")
+
+          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
+
+        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?
+
+          entities = JSON.parse(entities)
+
+          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
+
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, prepare_entities_for_json(children).to_json
+          when :html
+          end
+        end
+
+        # Neighbours
+
+        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
+
+          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
+
+        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?
+
+          entities = entities.split("|")
+
+          kb = get_kb 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
+
+        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?
+
+          entities = JSON.parse(entities)
+
+          kb = get_kb 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.each{|type, list| list.uniq!}
+
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, prepare_entities_for_json(neighbours).to_json
+          when :html
+          end
+        end
+
+        #{{{ OLD
+
+        get '/knowledge_base/entity/:name/:database/:entity' do
+          name = consume_parameter :name
+
+          database = consume_parameter :database
+          entity = consume_parameter :entity
+
+          kb = get_kb name
+          found = kb.identify database, entity
+          raise ParameterException, "Entity #{entity} was not found" unless found
+
+          list = kb.neighbours(database, found).values.select{|l| l.any?}.first.target_entity
+
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, list_json(list || [])
+          when :html
+            template_render('entity_partials/entity_list', :list => list)
+          end
+        end
+
+        get '/knowledge_base/entities/:name/:database' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entities = consume_parameter(:entities).split("|")
+
+          kb = get_kb name
+
+          entity_neighbours = {}
+          entities.each do |entity|
+            found = kb.identify database, entity
+            next unless found
+            list = kb.neighbours(database, found).values.select{|l| l.any?}.first.target_entity
+            entity_neighbours[entity] = list
+          end
+
+          case @format
+          when :json
+            content_type "application/json"
+            hash = {}
+            entity_neighbours.each do |entity, list|
+              hash[entity] = list_hash(list)
+            end
+            halt 200, hash.to_json
+          when :html
+            template_render('entity_partials/entity_list', :list => list)
+          end
+        end
+
+        get '/knowledge_base/entity/:name/:entity' do
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entity = consume_parameter :entity
+
+          kb = get_kb name
+
+          lists = {}
+          kb.all_databases.collect do |database|
+            found = kb.identify database, entity
+            next unless found
+            matches = kb.neighbours(database, found).values.select{|l| l.any?}.first
+            next if matches.nil?
+            lists[database] = matches.target_entity
+          end
+
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, lists.each{|database,entities| lists[database] = list_hash(entities || []) }.to_json
+          when :html
+            template_render('knowledge_base_partials/knowledge_base_matches', :matches => lists, :knowledge_base => kb)
+          end
+        end
+
+        #{{{ Hash 
+        
+        post '/knowledge_base/associations' do
+          knowledge_base = consume_parameter :knowledge_base
+          knowledge_base = get_knowledge_base(knowledge_base)
+
+          namespace = consume_parameter :namespace
+
+          databases = consume_parameter(:databases) || consume_parameter(:database)
+          databases = databases.nil? ? knowledge_base.all_databases : databases.split("|")
+
+          entities = consume_parameter :entities
+          entities = JSON.parse(entities)
+
+          subset = {}
+          databases.each do |database|
+            subset[database] = knowledge_base.subset(database, entities)
+          end
+
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, subset.each{|database,entities| subset[database] = list_hash(entities || []) }.to_json
+          when :html
+            template_render('entity_partials/associations', :matches => matches, :entities => entities)
+          end
+        end
+
+        post '/knowledge_base/neighbours' do
+          knowledge_base = consume_parameter :knowledge_base
+          knowledge_base = get_knowledge_base(knowledge_base)
+
+          namespace = consume_parameter :namespace
+
+          database = consume_parameter(:database)
+
+          entities = consume_parameter :entities
+          entities = JSON.parse(entities)
+
+          all_neighbours = {}
+          entities.collect{|source_type,list|
+            list.each do |entity|
+
+              target_type = knowledge_base.target_type(database)
+              source_type = knowledge_base.source_type(database)
+
+              neighbours = knowledge_base.neighbours(database, entity)
+
+              children = neighbours[:children] 
+              if children.any?
+                all_neighbours[target_type] ||= []
+                all_neighbours[target_type].concat children.target
+              end
+
+              parents = neighbours[:parents]
+              if parents and parents.any?
+                all_neighbours[source_type] ||= []
+                all_neighbours[source_type].concat parents.target
+              end
+            end
+          }
+
+          case @format
+          when :json
+            content_type "application/json"
+            halt 200, [].to_json if all_neighbours.empty?
+            entities = {}
+            all_neighbours.each do |type,list|
+              entities[type] = list
+            end
+
+            halt 200, all_neighbours.to_json
+          when :html
+            template_render('entity_partials/neighbours', :matches => matches, :neighbours => all_neighbours)
+          end
+        end
+      end
+    end
+  end
+end

data/lib/rbbt/rest/knowledge_base/helpers.rb

@@ -0,0 +1,57 @@
+require 'rbbt/util/misc'
+require 'rbbt/knowledge_base'
+
+module KnowledgeBaseRESTHelpers
+  class << self
+    attr_accessor :knowledge_base_dir, :knowledge_bases
+  end
+
+  self.knowledge_base_dir     = "var/knowledge_base"
+
+  def prepare_entities_for_json(entities)
+    case entities
+    when AnnotatedArray
+      list_hash(entities)
+    when Array
+      entities.inject([]){|acc,e| acc << prepare_entities_for_json(e); acc }
+    when Hash
+      hash = {}
+      entities.each do |key,values|
+        hash[key] = prepare_entities_for_json(values)
+      end
+      hash
+    when String
+      entities
+    end
+  end
+
+  def get_kb(name)
+    @knowledge_bases ||= IndiferentHash.setup({})
+    case name
+    when :genomics, "genomics"
+      @knowledge_bases[name] ||= Genomics.knowledge_base
+    else
+      @knowledge_bases[name] ||= KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
+    end
+  end
+
+  def get_knowledge_base(name, namespace = nil)
+    @knowledge_bases ||= IndiferentHash.setup({})
+    @knowledge_bases[name] ||= begin
+                                 kb = case 
+                                      when [:genomics, "genomics"].include?(name)
+                                        Genomics.knowledge_base
+                                      when (Misc.path_relative_to(settings.cache_dir, name) and File.exists?(name))
+                                        KnowledgeBase.new name
+                                      when KnowledgeBase.registry.include?(name)
+                                        KnowledgeBase.registry[name]
+                                      when Study.studies.include?(name)
+                                        Study.setup(name).knowledge_base
+                                      else
+                                        KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
+                                      end
+
+                                 namespace ? kb.version(namespace) : kb
+                               end
+  end
+end

data/lib/rbbt/rest/main.rb

@@ -42,7 +42,7 @@ module Sinatra
         set :allow_headers, ['URI']
 
         before do
-          Log.info("IP #{request.ip}: " << request.path_info << ". Params: " << Misc.remove_long_items(params).inspect)
+          Log.info("#{request.request_method} #{request.ip}: " << request.path_info << ". Params: " << Misc.fingerprint(params))
           process_common_parameters
 
           if profile
@@ -51,6 +51,7 @@ module Sinatra
         end
 
         after do
+          Log.info("#{request.request_method} #{request.ip}: " << request.path_info << ". Params: " << Misc.fingerprint(params) << "[#{response.status}]")
 
           if profile
             result = RubyProf.stop
@@ -71,11 +72,12 @@ module Sinatra
           send_file file
         end
 
-        get %r{/js/(.*)(.js)?} do
+        get %r{/js-find/(.*)(.js)?} do
           name = consume_parameter(:captures).first
 
           script_file = locate_javascript(name)
 
+          content_type 'text/javascript', :charset => 'utf-8'
           cache_control :public, :max_age => 360000 if production?
           send_file script_file
         end
@@ -93,7 +95,7 @@ module Sinatra
             Log.debug("Rendering stylesheets")
             renderer = Sass::Engine.new(Open.read(file), :filename => file, 
                                         :style => production? ? :compressed : nil, 
-                                        :debug_info => production? ? false : true)
+                                        :debug_info => development? ? true : false)
             renderer.render
           end
         end
@@ -102,6 +104,13 @@ module Sinatra
           template_render('main', params, 'main', :cache_type => :asynchronous)
         end
 
+        get '/main/*' do |file|
+          template = File.join 'main', file
+          name = template.gsub(/\//,' - ')
+          template_render(template, params, name, :cache_type => :asynchronous)
+        end
+
+
         get '/help/?:section?' do
           if params[:section]
             section = params[:section]
@@ -118,6 +127,10 @@ module Sinatra
             Open.read(File.join(settings.permalink_dir, params[:id]))
           end
         end
+
+        error RbbtRESTHelpers::TemplateMissing do |e|
+          halt 404, e.message
+        end
       end
     end
   end