rbbt-views 1.0.1 → 2.0.0

data/lib/rbbt/workflow/rest/client.rb

@@ -52,6 +52,8 @@ class RbbtRestClient
               RestClient.get(File.join(task.url, task.name.to_s, @remote_name) + "?_format=raw")
             when :tsv
               TSV.open(StringIO.new(RestClient.get(File.join(task.url, task.name.to_s, @remote_name) + "?_format=raw")))
+            when :annotations
+              Annotated.load_tsv(TSV.open(StringIO.new(RestClient.get(File.join(task.url, task.name.to_s, @remote_name) + "?_format=raw"))))
             else
               res = JSON.parse(RestClient.get(File.join(task.url, task.name.to_s, @remote_name) + "?_format=json"))
               res = TSV.setup(res) if task.result_type.to_sym == :tsv

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

@@ -1,11 +1,14 @@
+require 'rbbt/workflow/rest/render'
+require 'rbbt/workflow/rest/helpers'
+
 module Entity
 
   module REST
     include RbbtHTMLHelpers
 
     def rbbt_id
-      return "" unless self.annotations.include? :format and String === self.format
-      ([self.format.downcase, self] * "=").gsub(/[^\w]/,'_')
+      return "entity_id='#{self.id}'" unless self.annotations.include? :format and String === self.format
+      ([self.format.downcase, '"' + self + '"'] * "=").gsub(/[^"\w=]/,'_')
     end
 
     class << self
@@ -14,17 +17,19 @@ module Entity
 
     def link(text = nil, url = nil, options = {})
       return nil if self.nil?
+
       if Array === self
         text ||= self.name if self.respond_to? :name
         if Array === text
           translations = Misc.zip2hash(self, text)
-          self.collect{|e| e.link(translations[e], url, options)}
+          self.collect{|e| e.link(translations[e], url, options) unless e.nil?}.compact
         else
-          self.collect{|e| e.link(text, url, options)}
+          self.collect{|e| e.link(text, url, options) unless e.nil?}.compact
         end
       else
+        text = nil if String === text and text.empty?
+        text ||= self.name if self.respond_to? :name
 
-        text ||= self.name if self.respond_to? :name 
         text = self if text.nil? or text == :literal or text.to_s.strip.empty?
 
         klass = options[:class]
@@ -33,98 +38,90 @@ module Entity
         klass += " " << options[:extra_classes] || "" if options.include? :extra_classes
         klass += " " << html_class if self.respond_to? :html_class
 
-        type = self.respond_to?(:format)? annotation_types.last.to_s + 
+        main_annotation = options[:entity_type] || annotation_types.select{|a| Entity === a}.last.to_s
+        entity_type = self.respond_to?(:format)? main_annotation + 
           ":" + 
-          (self.format || "") : annotation_types.last.to_s
+          CGI.escape(self.format || "") : main_annotation
 
-        params = options[:params] || self.info.reject{|k,v| [:annotation_types, :format].include?(k)}
+        params = options[:params] || self.info(true).reject{|k,v| [:annotation_types, :format].include?(k)}
         params.merge! options[:extra_params] if options.include? :extra_params
+        params.merge! :entity_id => self.id if annotation_types.select{|annotation_type| annotation_type.respond_to?(:keep_id) and annotation_type.keep_id}.any?
 
         url ||= if options.include? :action
-                  File.join("/entity_action", type, options[:action].to_s, self)
+                  File.join("/entity_action", entity_type, options[:action].to_s, self)
                 else
-                  File.join("/entity", type, self)
+                  File.join("/entity", entity_type, self)
                 end
 
-        annotations_str = params.collect{|k,v| [k, CGI.escape(v.to_s)] * "="} * "&"
-        "<a class='#{klass}' #{rbbt_id} href='#{url + (annotations_str.any? ? '?' + annotations_str : "")}'>#{text}</a>"
+        annotations_str = params.collect{|k,v| v = v * "|" if Array === v; [k, CGI.escape(v.to_s)] * "="} * "&amp;"
+        "<a class='#{klass}' #{rbbt_id} href=\"#{annotations_str.empty? ? url : url + '?' + annotations_str}\" #{options.include?(:html_link_extra_attrs)? options[:html_link_extra_attrs] : "" } title='#{text}'>#{text}</a>"
       end
     end
 
-    def self.list_file(type, id, user = nil)
-      type = type.split(":").first if not type.nil? and type.index ':'
-      if production?
-        if user.nil?
-          File.join(Entity.entity_list_cache, type.to_s, id)
-        else
-          File.join(Entity.entity_list_cache, user.to_s, type.to_s, id)
-        end
+    def self.list_file(entity_type, id, user = nil)
+      entity_type = entity_type.split(":").first if not entity_type.nil? and entity_type.index ':'
+
+      id = CGI.unescape(id)
+      id = Misc.sanitize_filename(id)
+      raise "Ilegal list id: #{ id }" unless Misc.path_relative_to ".", File.join('.', id)
+
+      if user.nil?
+        File.join(Entity.entity_list_cache, entity_type.to_s, id)
       else
-        nil
+        File.join(Entity.entity_list_cache, user.to_s, entity_type.to_s, id)
       end
     end
 
     def self.list_files(user)
-      if production?
-        lists = {}
-        Dir.glob(File.join(Entity.entity_list_cache, user, '*', '*')).each do |file|
-          user, type, list = file.split("/")[-3..-1]
-          lists[type] ||= []
-          lists[type] << list
-        end
-        lists
-      else
-        {}
+      lists = {}
+      Dir.glob(File.join(Entity.entity_list_cache, user, '*', '*')).each do |file|
+        next if File.directory? file
+
+        file = File.expand_path(file)
+        raise "Ilegal path: #{ file }. Not relative to #{File.expand_path('.')}" unless Misc.path_relative_to(File.expand_path('.'), file)
+
+        user, entity_type, list = file.split("/")[-3..-1]
+        lists[entity_type] ||= []
+        lists[entity_type] << list
       end
+      lists
     end
 
-    def self.load_list(type, id, user = nil)
-      if production?
-        path = list_file(type, id, user)
-        path = list_file(type, id, :public) unless File.exists? path
-        path = list_file(type, id) unless File.exists? path
+    def self.load_list(entity_type, id, user = nil)
+      path = list_file(entity_type, id, user)
+      path = list_file(entity_type, id, :public) unless path != nil and File.exists? path
+      path = list_file(entity_type, id) unless path != nil and File.exists? path
 
-        Misc.lock path do
-          Annotated.load_tsv TSV.open(path)
-        end
-      else
-        @@list_cache ||= {}
-        @@list_cache[id]
+      begin
+        Annotated.load_tsv TSV.open(path)
+      rescue
+        nil
       end
     end
 
-    def self.save_list(type, id, list, user = nil)
-      if production?
-        path = list_file(type, id, user)
-
-        Misc.lock path do
-          begin
-            Open.write(path, Annotated.tsv(list, :all).to_s)
-          rescue
-            FileUtils.rm path if File.exists? path
-            raise $!
-          end
+    def self.save_list(entity_type, id, list, user = nil)
+      path = list_file(entity_type, id, user)
+
+      Misc.lock path do
+        begin
+          Open.write(path, Annotated.tsv(list, :all).to_s)
+        rescue
+          FileUtils.rm path if File.exists? path
+          raise $!
         end
-      else
-        @@list_cache ||= {}
-        @@list_cache[id] = list
       end
     end
 
 
-    def self.delete_list(type, id, user)
-      if production?
-        path = list_file(type, id, user)
-        "This list does not belong to #{ user }: #{[type, id] * ": "}" unless File.exists? path
-        Misc.lock path do
-          begin
-            FileUtils.rm path if File.exists? path
-          rescue
-            raise $!
-          end
+    def self.delete_list(entity_type, id, user)
+      path = list_file(entity_type, id, user)
+      "This list does not belong to #{ user }: #{[entity_type, id] * ": "}" unless File.exists? path
+      Misc.lock path do
+        begin
+          FileUtils.rm path if File.exists? path
+        rescue
+          raise $!
         end
-      else
-        @@list_cache.delete(id) if @@list_cache and @@list_cache.include? id
       end
     end
 
@@ -134,19 +131,24 @@ module Entity
 
       id ||= options[:id] || Misc.digest((self * "|").inspect)
 
+      id = clean_list_id(id)
 
       klass = (self.respond_to?(:format) and not self.format.nil?) ? self.format.gsub(/\s/,'_') : annotation_types.collect{|t| t.to_s.gsub(/\s/,'_')} * " "
 
       klass += " " << options[:extra_classes] if options.include? :extra_classes
       klass += " " << html_class if self.respond_to? :html_class
 
-      type = (self.respond_to?(:format) and not self.format.nil?) ? annotation_types.last.to_s + ":" + self.format : annotation_types.last.to_s
+      main_annotation = options[:entity_type] || annotation_types.select{|a| Entity === a}.last.to_s
+      entity_type = self.respond_to?(:format)? main_annotation + 
+        ":" + 
+        CGI.escape(self.format || "") : main_annotation
+
 
       Entity::REST.save_list(annotation_types.last.to_s, id, self) unless reuse
 
-      annotations_str = self.info.reject{|k,v| [:annotation_types, :format].include?(k)}.collect{|k,v| [k, CGI.escape(v.to_s)] * "="} * "&"
+      annotations_str = self.info(true).reject{|k,v| [:annotation_types, :format].include?(k)}.collect{|k,v| [k, CGI.escape(v.to_s)] * "="} * "&amp;"
 
-      "<a class='entity_list #{klass}' href='#{File.join("/entity_list", type, id) + (annotations_str.any? ? '?' + annotations_str : "")}'>#{text}</a>"
+      "<a class='entity_list #{klass}' href='#{File.join("/entity_list", entity_type, CGI.escape(id)) + (! annotations_str.empty? ? '?' + annotations_str : "")}' title='#{text}'>#{text}</a>"
     end
 
     def action_link(action, text = nil, inputs = {})
@@ -157,7 +159,7 @@ module Entity
         clean_inputs[k] = Array === v ? v * "," : v
       end
 
-      klass ||= "entity_action " + (self.respond_to?(:format)? self.format.gsub(/\s/,'_') : annotation_types.collect{|t| t.to_s.gsub(/\s/,'_')} * " ")
+      klass ||= "entity_action " + ((self.respond_to?(:format) and not self.format.nil?) ? self.format.gsub(/\s/,'_') : annotation_types.collect{|t| t.to_s.gsub(/\s/,'_')} * " ")
       klass += " " << options[:extra_classes] if options.include? :extra_classes
       klass += " " << html_class if self.respond_to? :html_class
 
@@ -172,19 +174,23 @@ module Entity
 
       text = id if text == :id
 
+      id = clean_list_id(id)
 
       klass = (self.respond_to?(:format) and not self.format.nil?) ? self.format.gsub(/\s/,'_') : annotation_types.collect{|t| t.to_s.gsub(/\s/,'_')} * " "
 
       klass += " " << options.delete(:extra_classes) if options.include? :extra_classes
       klass += " " << html_class if self.respond_to? :html_class
-
-      type = (self.respond_to?(:format) and not self.format.nil?)? annotation_types.last.to_s + ":" + self.format : annotation_types.last.to_s
+      
+      main_annotation = options[:entity_type] || annotation_types.select{|a| Entity === a}.last.to_s
+      entity_type = self.respond_to?(:format)? main_annotation + 
+        ":" + 
+        CGI.escape(self.format || "") : main_annotation
 
       Entity::REST.save_list(annotation_types.last.to_s, id, self) unless reuse
 
-      annotations_str = self.info.merge(options).reject{|k,v| [:annotation_types, :format].include?(k)}.collect{|k,v| [k, CGI.escape(v.to_s)] * "="} * "&"
+      annotations_str = self.info.merge(options).reject{|k,v| [:annotation_types, :format].include?(k)}.collect{|k,v| [k, CGI.escape(v.to_s)] * "="} * "&amp;"
 
-      "<a class='entity_list_action #{klass}' href='#{File.join("/entity_list_action", type, action, id) + (annotations_str.any? ? '?' + annotations_str : "")}'>#{text}</a>"
+      "<a class='entity_list_action #{klass}' href='#{File.join("/entity_list_action", entity_type, action, CGI.escape(id)) + (!annotations_str.empty? ? '?' + annotations_str : "")}' title='#{text}'>#{text}</a>"
     end
 
     def html_table(fields, workflow = nil, field_names = nil)

data/lib/rbbt/workflow/rest/finder.rb

@@ -0,0 +1,78 @@
+require 'sinatra/base'
+require 'rbbt/ner/finder'
+
+module Sinatra
+  module RbbtFinder
+
+    module Helpers
+      def finder_find(term)
+        results = settings.finder.find(term)
+
+        results.uniq.collect{|r| 
+            info = r.info
+            format_string = [info[:namespace], info[:format]].compact * ":"
+
+            info[:code] = r
+
+            if not format_string.empty?
+              info[:value] = r + " [#{format_string}]" 
+            else
+              info[:value] = r
+            end
+
+            score = info.delete :score
+
+            if Array === score
+              info[:score] = score[0]
+              info[:best] = score[1]
+            end
+
+            info 
+          }.sort_by{|i| i[:score] || 0}.reverse
+      end
+    end
+
+    def self.registered(app)
+      app.helpers RbbtFinder::Helpers
+
+      app.get '/find' do
+        return workflow_render('find.haml') if params[:term].nil?
+
+        Log.debug "find: #{params.inspect}"
+        term = params[:term]
+        sorted_results = finder_find(term)
+
+        raise "No finder defined" if app.finder.nil?
+        if request.xhr?
+          content_type "application/json" 
+          sorted_results.to_json
+        else
+          i = sorted_results.first
+          raise "Term not recognized: #{ term }" if i.nil?
+          redirect_to_entity(i[:code], i[:format], i[:namespace])
+        end
+      end
+
+      app.post '/find' do
+        term = params[:term]
+        if term =~ /(.*) \[(.*)\]$/
+          term = $1
+          namespace, format = $2.split(":")
+          format, namespace = namespace, nil if format.nil?
+
+          redirect_to_entity(term, format, namespace)
+        else
+          sorted_results = finder_find(term)
+          i = sorted_results.first
+          raise "Term not recognized: #{ term }" if i.nil?
+          redirect_to_entity(i[:code], i[:format], i[:namespace])
+        end
+      end
+
+    end
+  end
+
+  register RbbtFinder
+end
+
+

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

@@ -1,87 +1,328 @@
+require 'rbbt/workflow/annotate'
+require 'yui/compressor'
 
 module RbbtHTMLHelpers
-  def input(type, name, options = {})
-    id, hide, value, klass, default, description = Misc.process_options options, :id, :hide, :value, :class, :default, :description
-    str = "<div class='form_input' id='#{ id }'>"
+  def clean_list_id(list_id)
+    list_id.gsub('/', '_')
+  end
 
-    if hide
-      str << "<input #{"id='#{ id }'" if id} type='hidden' name='#{ name }' #{"class='#{ klass }'" if klass} #{"value='#{ value }'" if value}/>" << '</div>' << "\n"
-      return str
+  def log(status, message)
+    if Step.log_relay_step
+      Step.log_relay_step.log status, message
+    else
+      Log.warn "[#{ status }] #{ message }"
     end
+  end
+
+  def included(base)
+    base.include AnnotatedModule
+  end
+
+  def format_float(float)
+    "%.3f" % float
+  end
+
+  def redirect_to_entity(entity, format, namespace)
+    entity_type = Entity.formats[format]
+
+    entity_options = []
+
+    if defined? Organism and 
+      entity_type.annotations.include? :organism and 
+      ((String === namespace or Symbol === namespace) and 
+       Organism.organisms.include? namespace.to_s or Organism.organisms.include? namespace.to_s.split("/").first)
+      entity_options << ["organism", namespace] * "=" 
+    end
+
+    entity_options = entity_options.empty? ? "" : "?" + entity_options * "&"
+
+    if format
+      redirect "/entity/#{ entity_type.to_s }:#{ format }/#{ entity }#{entity_options}"
+    else
+      redirect "/entity/#{ entity_type.to_s }/#{ entity }#{entity_options}"
+    end
+  end
+
+  def user_action_defaults
+    @@user_action_defaults ||= Persist.open_tokyocabinet(settings.user_action_defaults, false, :marshal)
+  end
+
+  def add_user_defaults(user, entity, action, params)
+    return params if params.delete :no_defaults
+    key = [user, entity, action] * ":"
+
+    user_action_defaults.read_and_close do
+      if user_action_defaults.include?(key) and not user_action_defaults[key] == :clear and not user_action_defaults[key].nil?
+        Log.debug("Loading user defaults for #{key}")
+        new = (user_action_defaults[key] || {} ).dup.merge(params)
+        new.each do |key, value|
+          next if params.include? key
+          params[key] = value
+        end
+      end
+    end
+
+    params
+  end
 
+  def save_user_defaults(user, entity, action, params)
+    key = [user, entity, action] * ":"
+    clear = user_action_defaults.read_and_close do user_action_defaults[key] == :clear end
+
+    if clear
+      Log.debug("Effectively clearing user defaults for #{key}")
+      user_action_defaults.write_and_close do
+        user_action_defaults.delete key
+      end
+    else
+      Log.debug("Saving user defaults for #{key}")
+      user_action_defaults.write_and_close do
+        user_action_defaults[key] = Hash[*(params.collect{|k,v| [k,v]}.flatten(1))]
+      end
+    end
+  end
+
+  def clear_user_defaults(user, entity, action)
+    key = [user, entity, action] * ":"
+    Log.debug("Clearing user defaults for #{key}")
+    user_action_defaults.write_and_close do
+      user_action_defaults[key] = :clear
+    end
+  end
+
+  def parameter_controls(workflow = nil, values = {}, &block)
+    o = Object.new
+    o.extend AnnotatedModule
+    o.instance_eval &block
+
+    inputs = o.inputs
+    input_types = o.input_types
+    input_defaults = o.input_defaults
+    input_options = o.input_options
+
+    hidden_inputs = []
+    inputs.each do |input|
+      if values[input].nil? and input_defaults.include? input
+        values[input] = input_defaults[input]
+      end
+      hidden_inputs << input if input_options.include? input and input_options[input].delete :hide
+    end
+
+    workflow_partial('partials/_form', workflow, :hide_inputs => hidden_inputs, :inputs => inputs, :input_defaults => input_defaults, :input_options => input_options, :input_types => input_types, :values => values, :action => headers["AJAX-URL"], :klass => 'task', :method => 'get')
+  end
+
+  def link_to_resource(filename = nil, text = nil, type = nil, options = {})
+    case
+    when filename.nil?
+      filename = File.basename(TmpFile.tmp_file)
+    when filename[0] == "."[0]
+      extension = filename
+      filename = File.basename(TmpFile.tmp_file) + extension
+    end
+
+    text ||= filename
+
+    filename = Misc.sanitize_filename(filename)
+    f = File.join(settings.file_dir, filename)
+    FileUtils.mkdir_p(File.dirname(f))
+    yield(f)
+
+    type ||= :link
     case type
-    when :boolean
-      not_value = ! value
-      str << "<label #{"for='#{ id }" if id}'><span class='input_name'>#{ name }</span>#{": <span class='input_description'>#{ description }</span>" if description}</label>" << "\n"
-      str << "<input type='radio' id='input_#{id}_true' name='#{ name }' value='true' #{"checked='true'" if value}>" << "\n"
-      str << "<label type='radio_option radio_true' for='input_#{id}_true' name='#{ name }'>true</label>" << "\n"
-      str << "<input type='radio' id='input_#{id}_false' name='#{ name }' value='false' #{"checked='false'" if not value}>" << "\n"
-      str << "<label type='radio_option radio_false' for='input_#{id}_false' name='#{ name }'>false</label>" << "\n"
-      str << "</div>"
-      str
-    when :string, :float, :integer
-      str << "<label #{"for='#{ id }" if id}'><span class='input_name'>#{ name }</span>#{": <span class='input_description'>#{ description }</span>" if description}#{": <span class='input_default'>(Default: #{ default })</span>" if default}</label>" << "\n"
-      str << "<input #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} #{"id='#{ id }'" if id} name='#{ name }' #{"value='#{ value }'" if value}/>" << "\n"
-      str << "</div>"
-      str
-    when :tsv, :array, :text
-      str << "<label #{"for='#{ id }" if id}'><span class='input_name'>#{ name }</span>#{": <span class='input_description'>#{ description }</span>" if description}#{": <span class='input_default'>(Default: #{ default })</span>" if default}</label>" << "\n"
-      str << "<p>"
-      str << "<input type='file' #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} #{"id='input_#{ id }_tsv_file'" if id} name='#{ name }_param_file' #{"value='#{ value }'" if value}/>" << "\n"
-      str << "<span class='tsv_textarea_note note'>(or use text area bellow)</span>"
-      str << "</p>"
-      str << "<textarea #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} name='#{ name }' #{"id='input_#{ id }'" if id}></textarea>"
-      str << "</div>"
-      str
+    when :image
+      "<img src='/files/#{ filename }' class='file_resource'/>"
+    when :link
+      "<a href='/files/#{ filename }' class='file_resource'>#{ text }</a>"
+    when :linked_image
+      "<a href='/files/#{ filename }' class='file_resource' target='_blank'><img src='/files/#{ filename }' class='file_resource'/></a>"
+    when :zoomable_image
+      id = options[:id] || Misc.digest(filename)
+      width, height= [300, 300]
+      "<div class='zoomable_image'><img id='#{id}' style='width:#{width}px; height:#{height}px' rel='/files/#{ filename }' src='/files/#{ filename }' class='file_resource'/></div>"
+    when :mapped_image
+      mapid = options[:mapid] || options[:id] + '_map'
+      width, height= [300, 300]
+      mapfile = f.sub(/\.[^.]+$/, '.html')
+      "<div class='mapped_image'>#{Open.read(mapfile)}<img class='has_map' usemap='##{mapid}' rel='/files/#{ filename }' src='/files/#{ filename }' class='file_resource'/></div>"
+    else
+      raise "Type not understood: #{ type }"
     end
   end
 
-  def input(type, name, options = {})
-    id, hide, value, klass, default, description, select_options = Misc.process_options options, :id, :hide, :value, :class, :default, :description, :select_options
-    str = "<div class='form_input' id='#{ id }'>"
+  def html_options_str(html_options = {})
+    return "" if html_options.nil? or html_options.empty?
+    html_options.collect{|k,v| 
+      case 
+      when (k.nil? or v.nil? or (String === v and v.empty?))
+        nil
+      when String === v
+        [k,"'" + v + "'"] * "="
+      when Symbol === v
+        [k,"'" + v.to_s + "'"] * "="
+      when TrueClass === v
+        [k,"'" + k.to_s + "'"] * "="
+      else
+        nil
+      end
+    }.compact * " "
+  end
+
+  def form_input(type, name, options = {})
+    id, label, hide, value, klass, default, description, input_options, array_separator = Misc.process_options options, 
+      :id, :label, :hide, :value, :class, :default, :description, :input_options, :array_separator
+
+    html_options ||= (input_options.nil? ? nil : input_options[:html_options]) || {}
+
+    if id and not id.empty?
+      str = "<div class='form_input' id='#{ id }'>"
+    else
+      str = "<div class='form_input'>"
+    end
+
+    array_separator ||= '|'
+    label ||= name
+
+    hide ||= html_options.delete :hidden
 
     if hide
-      str << "<input #{"id='#{ id }'" if id} type='hidden' name='#{ name }' #{"class='#{ klass }'" if klass} #{"value='#{ value }'" if value}/>" << '</div>' << "\n"
+      value = value * array_separator if Array === value
+
+      html_options.merge! :id => id, 
+        :type => 'hidden', 
+        :name => name, 
+        :value => value.to_s,
+        :class  => [html_options[:class], klass].compact * " "
+
+      str = "<input #{html_options_str(html_options)}/>" << "\n"
       return str
     end
 
     case type
     when :select
-      str << "<label #{"for='#{ id }" if id}'><span class='input_name'>#{ name }</span>#{": <span class='input_description'>#{ description }</span>" if description}</label>" << "\n"
-      str << "<select id='input_#{id}_true' name='#{ name }'>" << "\n"
+      str << "<label #{html_options_str({:for => id})}>"
+      str << "<span class='input_name'>#{ label }</span>"
+      str << ": <span class='input_description'>#{ description }</span>" if description
+      str << "</label>" << "\n"
+
+      str << "<select #{html_options_str(html_options.merge :name => name, :id => ((id and not id.empty?) ? "input_#{id}_select" : nil ))}>" << "\n"
+
+      select_options = input_options.nil? ? nil : input_options[:select_options]
       if not select_options.nil?
         select_options.each do |option|
           option, option_name = option if Array === option
           option_name ||= option
-          str << "<option id='input_#{id}_option_#{option.to_s}' value='#{option.to_s}' #{option.to_s == value.to_s ? "selected=selected" : "" }>" << option_name.to_s << "</option>" << "\n"
+          str << "<option #{html_options_str(html_options.merge :value => option, :selected => option.to_s == value.to_s)}>" << option_name.to_s << "</option>" << "\n"
         end
       end
+
+      if html_options["attr-allow-empty"]
+        str << "<option #{html_options_str(html_options.merge :value => "none", :selected => "none" == value.to_s)}>none</option>" << "\n"
+      end
+
       str << "</select>" << "\n"
       str << "</div>"
       str
     when :boolean
-      not_value = ! value
-      str << "<label #{"for='#{ id }" if id}'><span class='input_name'>#{ name }</span>#{": <span class='input_description'>#{ description }</span>" if description}</label>" << "\n"
-      str << "<input type='radio' id='input_#{id}_true' name='#{ name }' value='true' #{"checked='true'" if value}>" << "\n"
-      str << "<label type='radio_option radio_true' for='input_#{id}_true' name='#{ name }'>true</label>" << "\n"
-      str << "<input type='radio' id='input_#{id}_false' name='#{ name }' value='false' #{"checked='false'" if not value}>" << "\n"
-      str << "<label type='radio_option radio_false' for='input_#{id}_false' name='#{ name }'>false</label>" << "\n"
+      value = false if value == "false"
+      default = value unless value.nil?
+      default = false if default == "false"
+      default = true if default == "true"
+
+      check_true = default and %w(true yes y).include? default.to_s.downcase
+      check_false = (default != nil and %w(false no n).include?(default.to_s.downcase))
+
+      str << "<label #{"for='#{ id }'" if id}>"
+      str << "<span class='input_name'>#{ label }</span>"
+      str << "#{": <span class='input_description'>#{ description }</span>" if description}</label>" << "\n"
+
+      str << "<input type='radio' #{check_true ? "checked=checked " : ""}#{html_options_str(html_options.merge :name => name, :value => 'true', :id => ((id and not id.empty?) ? "input_#{id}_true" : nil))}>" << "\n"
+      str << "<label #{html_options_str(html_options.merge :for => ((id and not id.empty?) ? "input_#{id}_true" : nil), :class => [html_options[:class], 'radio_option radio_true'].compact * " ")}>true</label>" << "\n"
+
+      str << "<input type='radio' #{check_false ? "checked=checked " : ""}#{html_options_str(html_options.merge :name => name, :value => 'false', :id => ((id and not id.empty?) ? "input_#{id}_false" : nil))}>" << "\n"
+      str << "<label #{html_options_str(html_options.merge :for => ((id and not id.empty?) ? "input_#{id}_false" : nil), :class => [html_options[:class], 'radio_option radio_false'].compact * " ")}>false</label>" << "\n"
       str << "</div>"
       str
     when :string, :float, :integer
-      str << "<label #{"for='#{ id }" if id}'><span class='input_name'>#{ name }</span>#{": <span class='input_description'>#{ description }</span>" if description}#{": <span class='input_default'>(Default: #{ default })</span>" if default}</label>" << "\n"
-      str << "<input #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} #{"id='#{ id }'" if id} name='#{ name }' #{"value='#{ value }'" if value}/>" << "\n"
+      value = value * array_separator if Array === value
+      str << "<label #{"for='#{ id }'" if id}><span class='input_name'>#{ label }</span>#{": <span class='input_description'>#{ description }</span>" if description}#{": <span class='input_default'>(Default: #{ default })</span>" if default}</label>" << "\n"
+      str << "<input #{html_options_str(html_options)} #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} #{"id='#{ id }'" if id} name='#{ name }' #{"value='#{ value }'" if value}/>" << "\n"
       str << "</div>"
       str
     when :tsv, :array, :text
-      str << "<label #{"for='#{ id }" if id}'><span class='input_name'>#{ name }</span>#{": <span class='input_description'>#{ description }</span>" if description}#{": <span class='input_default'>(Default: #{ default })</span>" if default}</label>" << "\n"
+      str << "<label #{"for='#{ id }'" if id}><span class='input_name'>#{ label }</span>#{": <span class='input_description'>#{ description }</span>" if description}#{": <span class='input_default'>(Default: #{ default })</span>" if default}</label>" << "\n"
       str << "<p>"
-      str << "<input type='file' #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} #{"id='input_#{ id }_tsv_file'" if id} name='#{ name }_param_file' #{"value='#{ value }'" if value}/>" << "\n"
+      str << "<input #{html_options_str(html_options)} type='file' #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} #{"id='input_#{ id }_tsv_file'" if id} name='#{ name }_param_file' #{"value='#{ value }'" if value}/>" << "\n"
       str << "<span class='tsv_textarea_note note'>(or use text area bellow)</span>"
       str << "</p>"
-      str << "<textarea #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} name='#{ name }' #{"id='input_#{ id }'" if id}></textarea>"
+      str << "<textarea #{"class='#{klass ? klass : "#{ name } #{ type }" }'"} name='#{ name }' #{"id='input_#{ id }'" if id}>#{Array === value ? value * "\n" : value}</textarea>"
       str << "</div>"
       str
     end
   end
+
+  def table(rows, header = nil, options = {}) 
+    workflow_partial('partials/_table', StudyExplorer, nil, options.merge(:rows => rows, :header => header))
+  end
+
+  def followed_users(user)
+    settings.followed_users[user] || []
+  end
+
+  def record_js(file)
+    @js_files << file
+  end
+
+  def serve_js(compress = true)
+    res = if production? and compress
+
+      md5 = Misc.digest(@js_files * ",")
+      filename = File.join(settings.file_dir, "all_js-#{md5}.js")
+
+      if not File.exists?(filename)
+        text = @js_files.collect{|file| 
+          file += '.js' unless file =~ /.js$/
+          if file =~ /^\/js\/entity\/(.*?)\/(.*?)\/(.*)/
+            entity_type, format = $1.split ":"
+            entity = setup_entity(entity_type, format, $2)
+            path = locate_file(WorkflowREST.workflows.last, nil, File.join("js", $3), entity)
+          else
+            path = begin
+                     locate_file(WorkflowREST.workflows.last, nil, file.sub(/^\//,'')).find
+                   rescue
+                     locate_file(WorkflowREST.workflows.last, nil, File.join('public', file)).find
+                   end
+          end
+          Open.read(path)
+        } * "\n"
+
+
+        FileUtils.mkdir_p File.dirname(filename) unless File.exists? File.dirname(filename)
+        Open.write(filename, YUI::JavaScriptCompressor.new(:munge => false).compress(text))
+      end
+
+      "<script src='/files/#{File.basename(filename)}' type='text/javascript'></script>"
+    else
+      @js_files.collect{|file|
+        file += '.js' unless file =~ /.js$/
+          "<script src='#{ file }' type='text/javascript'></script>"
+      } * "\n"
+    end
+    @js_files.clear
+    res
+  end
+
+  def record_css(file)
+    @css_files << file
+  end
+
+  def serve_css
+    res = @css_files.collect{|file|
+      file += '.css' unless file =~ /.css$/
+      "<link href='#{file}' rel='stylesheet' type='text/css' />"
+    } * "\n"
+    @css_files.clear
+    res
+  end
+
+
 end