rbbt-views 0.1.2 → 1.0.0

data/lib/rbbt/workflow/rest.rb

@@ -10,9 +10,10 @@ require 'sinatra/authorization'
 require 'rbbt/workflow/rest/util.rb'
 require 'rbbt/workflow/rest/render.rb'
 require 'rbbt/workflow/rest/auth.rb'
+require 'rbbt/workflow/rest/email.rb'
+require 'rbbt/workflow/rest/helpers.rb'
 
 module WorkflowREST
-  extend Resource
 
   class << self
     attr_accessor :workflows
@@ -20,18 +21,21 @@ module WorkflowREST
   end
   self.workflows = []
 
+
   def self.setup
     configure do
-      Compass.add_project_configuration(WorkflowREST.share.views.compass["compass.config"].find.dup.to_s)
+      Compass.add_project_configuration(Rbbt.share.views.compass["compass.config"].find.dup.to_s)
     end
 
     Sinatra.module_eval do
       helpers Sinatra::SinatraRbbt
       enable :sessions
+      enable :static
 
       before do
         @file_cache = {}
         @result_cache = {}
+        headers "AJAX-URL" => request.env["REQUEST_URI"]
       end
 
       after do
@@ -44,40 +48,85 @@ module WorkflowREST
           "Workflow Explorer"
         end
 
-        def authorize(login, password)
-          login == "miki" && password == "miki"
-        end
-
         def check_user(user)
           login_required
           request.env['REMOTE_USER'] == user || throw(:halt, [ 401, 'Authorization Required' ])
         end
       end
+    end
 
+    set :public_folder, RbbtHTMLHelpers.locate_file(nil, nil, 'public/').find
+
+    begin
+      set :users, RbbtHTMLHelpers.locate_file(nil, nil, 'config/users').yaml
+    rescue
+      if Rbbt.etc.web_users.exists?
+        set :users, Rbbt.etc.web_users.yaml
+      else
+        set :users, {}
+      end
     end
 
-    set :public_folder, Sinatra::SinatraRbbt.locate_file(nil, nil, 'public/').find
+    if production?
+      before do
+        cache_control :public, :must_revalidate, :max_age => 60
+      end
+      Log.severity = 0
+    end
 
     get '/stylesheets/:name.css' do
-      file = locate_file(nil, nil, File.join("compass", params[:name] + '.sass'))
-      css = Persist.persist("Stylesheet:#{file}", :string, :persist => ENV["RACK_ENV"].to_s == 'production', :dir => 'cache') do
+      file = locate_file(WorkflowREST.workflows.last, nil, File.join("compass", params[:name] + '.sass'))
+
+      content_type 'text/css', :charset => 'utf-8'
+      cache('css', params) do
         renderer = Sass::Engine.new(file.read)
-        renderer.render.to_s
+        renderer.render
       end
-      content_type 'text/css', :charset => 'utf-8'
-      css
     end
 
     get '/js/:name.js' do
       content_type 'text/css', :charset => 'utf-8'
-      file = locate_file(nil, nil, File.join("js", params[:name] + '.js'))
-      file.read
+      send_file locate_file(nil, nil, File.join("js", params[:name] + '.js')).find
     end
 
     get '/entity/:type/:entity' do
       type = params[:type]
 
-      entity_render(type, params)
+      visualization_parameters = get_visualization_parameters(params)
+      cache("Entity:", :params => params, :visualization_params => visualization_parameters, :user => user) do
+        entity_render(type, params.merge(visualization_parameters))
+      end
+    end
+
+    get '/entity_list/:type/:id' do
+      type = params.delete "type"
+      visualization_parameters = get_visualization_parameters(params)
+
+      cache("Entity List:", :params => params, :type => type, :visualization_params => visualization_parameters, :user => user) do
+        entity_list_render(type, params.merge(visualization_parameters))
+      end
+    end
+
+    get '/entity_action/:type/:action/:entity' do
+      type = params.delete "type"
+      action = params.delete "action" 
+
+      visualization_parameters = get_visualization_parameters(params)
+
+      cache("Entity Action [#{action}]:", :params => params, :type => type, :action => action, :visualization_params => visualization_parameters, :user => user) do
+        entity_action_render(type, action, params.merge(visualization_parameters))
+      end
+    end
+
+    get '/entity_list_action/:type/:action/:id' do
+      type = params.delete "type"
+      action = params.delete "action" 
+
+      visualization_parameters = get_visualization_parameters(params)
+
+      cache("Entity List Action [#{action}]:", :params => params, :type => type, :action => action, :visualization_params => visualization_parameters, :user => user) do
+        entity_list_action_render(type, action, params.merge(visualization_parameters))
+      end
     end
 
   end
@@ -87,12 +136,6 @@ module WorkflowREST
     task_name = task_name.to_s
     workflow_name = workflow.to_s
 
-    # MOVE!!!!
-    get File.join("/plugins", workflow_name, "*") do
-      file = params[:splat].first
-      send_file Sinatra::SinatraRbbt.locate_file(workflow, nil, 'plugins/' + file)
-    end
-
     # context info
     delete File.join("/context", workflow_name, ":task") do
       task, jobname = params.values_at :task
@@ -118,7 +161,7 @@ module WorkflowREST
       when visualization_parameters[:_format] == "raw"
         task_info.collect{|k,v| [k,v] * "\t"} * "\n"
       when visualization_parameters[:_format] == "html"
-        workflow_render(workflow, task_name, "task_info", workflow.task_info(task_name).merge(visualization_parameters).merge(:task_info => task_info))
+        workflow_render("task_info", workflow, task_name, workflow.task_info(task_name).merge(visualization_parameters).merge(:task_info => task_info))
       end
     end
 
@@ -131,7 +174,7 @@ module WorkflowREST
 
       job_list = workflow.jobs(task_name, user + "/").collect{|jobname| File.basename(jobname)}
 
-      workflow_render(workflow, task_name, "job_list", visualization_parameters.merge(:workflow => workflow, :task_name => task_name, :job_list => job_list))
+      workflow_render("job_list", workflow, task_name, visualization_parameters.merge(:workflow => workflow, :task_name => task_name, :job_list => job_list))
     end
 
 
@@ -147,7 +190,7 @@ module WorkflowREST
         result = workflow.job(task_name, "EXEC", inputs.dup).exec
         result = paginate(result, params[:_page]) if params.include? :_page
 
-        workflow_render_result(workflow, task_name, result, visualization_parameters.merge(:inputs => inputs))
+        workflow_render_result(result, workflow, task_name, visualization_parameters.merge(:inputs => inputs))
 
         # direct job issuing and redirection when job has all paramteres
       when has_all_inputs(workflow, task_name, inputs)
@@ -173,7 +216,7 @@ module WorkflowREST
 
         redirect redirection
       else
-        workflow_render(workflow, task_name, "form", workflow.task_info(task_name).merge(visualization_parameters))
+        workflow_render("form", workflow, task_name, workflow.task_info(task_name).merge(visualization_parameters))
       end
     end
 
@@ -189,7 +232,7 @@ module WorkflowREST
 
       when :exec
         result = workflow.job(task_name, real_jobname, inputs.dup).exec
-        workflow_render_result(workflow, task_name, result, visualization_parameters.merge(:inputs => inputs))
+        workflow_render_result(result, workflow, task_name, visualization_parameters.merge(:inputs => inputs))
 
       when :synchronous, :asynchronous
         job = workflow.job(task_name, real_jobname, inputs)
@@ -197,7 +240,22 @@ module WorkflowREST
         if type.to_sym == :synchronous
           job.run
         else
+          email = get_email(params)
           job.fork
+          if can_send_email? and not (email.nil? or email.empty?) and valid_email?(email)
+            Log.debug "Monitoring #{job.name} completion for email notification"
+            Process.fork do
+              while not job.done?
+                sleep 5
+              end
+              case
+              when job.error?
+                send_email(workflow, email, "Job #{job.name} failed", job.messages.last)
+              else
+                send_email(workflow, email, "Job #{job.name} succeded", "")
+              end
+            end
+          end
         end
 
         return job.name if visualization_parameters[:_format] == "json"
@@ -234,7 +292,7 @@ module WorkflowREST
         if visualization_parameters[:_format] == "html"
           content_type "text/html"
           status 500
-          return workflow_render(workflow, task_name, "error", workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs]))
+          return workflow_render("error", workflow, task_name, workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs]))
         else
           status 500
           content_type "text/plain"
@@ -248,7 +306,7 @@ module WorkflowREST
           content_type "text/html"
           status 202
           @rbbt_refresh = 30 unless step.error?
-          return workflow_render(workflow, task_name, "wait", workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs]))
+          return workflow_render("wait", workflow, task_name, workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs]))
         else
           status 202
           step.status
@@ -257,24 +315,42 @@ module WorkflowREST
         # DONE
       else
 
-        case
-        when visualization_parameters[:_format] == "html"
-          result = step.load
-          workflow_render_result(workflow, task_name, result, workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs], :result => result))
-
-        when visualization_parameters[:_format] == "json"
-          content_type "application/json"
-          result = step.load
-          result = paginate(result, visualization_parameters[:_page]) if visualization_parameters.include? "_page"
-          result.to_json
-
-        else
-          content_type "text/plain"
-          result = step.load
-          result = paginate(result, visualization_parameters[:_page]) if visualization_parameters.include? "_page"
-          result.to_s
-        end
-
+        cache("Job Result:", 
+              :visualization_parameters => visualization_parameters,
+              :workflow => workflow.to_s,
+              :task_name => task_name,
+              :jobname => jobname,
+              :user => user
+             ) do
+               case
+               when visualization_parameters[:_format] == "html"
+                 result = step.load
+                 workflow_render_result(result, workflow, task_name, workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs], :result => result))
+
+               when visualization_parameters[:_format] == "json"
+                 content_type "application/json"
+                 result = step.load
+                 result = paginate(result, visualization_parameters[:_page]) if visualization_parameters.include? "_page"
+
+                 if TSV === result
+                   result.dup.to_json
+                 else
+                   result.to_json
+                 end
+
+               else
+                 content_type "text/plain"
+                 result = step.load
+                 result = paginate(result, visualization_parameters[:_page]) if visualization_parameters.include? "_page"
+                 case
+                 when Array === result
+                   result * "\n"
+                 else
+                   result.to_s
+                 end
+               end
+
+             end
       end
     end
 
@@ -296,7 +372,7 @@ module WorkflowREST
       when visualization_parameters[:_format] == "raw"
         info.collect{|k,v| [k,v] * "\t"} * "\n"
       when visualization_parameters[:_format] == "html"
-        workflow_render(workflow, task_name, "info", visualization_parameters.merge(:info => info))
+        workflow_render("info", workflow, task_name, visualization_parameters.merge(:info => info))
       end
     end
 
@@ -318,7 +394,7 @@ module WorkflowREST
       when visualization_parameters[:_format] == "raw"
         dependencies.collect{|task, job| [task, job] * "\t"} * "\n"
       when visualization_parameters[:_format] == "html"
-        workflow_render(workflow, task_name, "dependencies", visualization_parameters.merge(:dependencies => dependencies, :workflow => workflow, :task_name => task_name, :jobname => jobname))
+        workflow_render("dependencies", workflow, task_name, visualization_parameters.merge(:dependencies => dependencies, :workflow => workflow, :task_name => task_name, :jobname => jobname))
       end
     end
 
@@ -340,7 +416,7 @@ module WorkflowREST
       when visualization_parameters[:_format] == "raw"
         files * "\n"
       when visualization_parameters[:_format] == "html"
-        workflow_render(workflow, task_name, "files", visualization_parameters.merge(:files => files, :workflow => workflow, :task_name => task_name, :jobname => jobname))
+        workflow_render("files", workflow, task_name, visualization_parameters.merge(:files => files, :workflow => workflow, :task_name => task_name, :jobname => jobname))
       end
     end
 
@@ -398,15 +474,11 @@ module WorkflowREST
 
 
   def self.add_workflows(*workflows)
-    self.workflows.concat workflows
+    self.workflows.concat workflows.select{|wf| Module === wf}
     self.workflows.uniq!
-    get '/' do
-      visualization_parameters = get_visualization_parameters(params)
-      workflow_render(nil, nil, "workflow_list", visualization_parameters.merge(:workflows => WorkflowREST.workflows))
-    end
-
+    
+    self.workflows.each do |workflow|
 
-    WorkflowREST.workflows.each do |workflow|
       get File.join('/', workflow.to_s) do
         visualization_parameters = get_visualization_parameters(params)
 
@@ -414,10 +486,15 @@ module WorkflowREST
         if visualization_parameters[:_format] and visualization_parameters[:_format].to_sym == :json
           tasks.to_json
         else
-          workflow_render(workflow, nil, "task_list", visualization_parameters.merge(:workflow => workflow, :tasks => tasks))
+          workflow_render("task_list", workflow, nil, visualization_parameters.merge(:workflow => workflow, :tasks => tasks))
         end
       end
 
+      get File.join("/plugins", workflow.to_s, "*") do
+        file = params[:splat].first
+        send_file RbbtHTMLHelpers.locate_file(workflow, nil, 'plugins/' + file)
+      end
+
       workflow.asynchronous_exports.each do |name|
         WorkflowREST.add_task workflow, name, :asynchronous
       end
@@ -430,6 +507,14 @@ module WorkflowREST
         WorkflowREST.add_task workflow, name, :exec
       end
 
+      if workflow.libdir.lib["sinatra.rb"].exists?
+        require workflow.libdir.lib["sinatra.rb"].find
+      end
+    end
+
+    get '/' do
+      visualization_parameters = get_visualization_parameters(params)
+      workflow_render("front", visualization_parameters.merge(:workflows => WorkflowREST.workflows.select{|w| Module === w}))
     end
 
   end

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

@@ -38,12 +38,15 @@ module Sinatra
       end
 
       app.post '/login' do
+        Log.debug "Loggin: #{params.inspect}"
         if options.users.include? params[:user] and options.users[params[:user]] == params[:pass]
+          Log.debug "Loggin Successful"
           session[:authorized] = true
           session[:user] = params[:user]
           session[:context] = nil
           redirect '/'
         else
+          Log.debug "Loggin Failed"
           session[:authorized] = false
           session[:user] = nil
           session[:context] = nil
@@ -58,8 +61,6 @@ module Sinatra
         redirect '/'
       end
 
-
-
     end
   end
 

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

@@ -47,8 +47,11 @@ class RbbtRestClient
           end
 
           def load
-            if task.result_type.to_sym == :string
+            case task.result_type.to_sym
+            when :string
               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")))
             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/email.rb

@@ -0,0 +1,23 @@
+require 'rbbt'
+require 'rbbt/util/misc'
+module Sinatra
+  module SinatraRbbt
+
+    def valid_email?(email)
+      !!(email =~ /\w@\w/)
+    end
+
+    def can_send_email?
+      Rbbt.etc.smtp_config.exists?
+    end
+
+    def send_email(workflow, to, subject, message)
+      Log.low "Sending email to: #{ to }. Subject: #{ subject }"
+      raise "Cannot send emails, config is missing" if not can_send_email?
+      mail_options = Rbbt.etc.smtp_config.yaml
+      Misc.send_email("no-replay@#{workflow.to_s}", to, subject, message, mail_options)
+    end
+  end
+end
+
+ 

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

@@ -1,77 +1,102 @@
-module EntityOLD
-  ENTITIES = {}
-  METHODS = {}
-  SYNONYMS = {}
-
-  def self.tsv_sort(&block)
-    METHODS[:tsv_sort] = block
-  end
-
-  def self.sort(&block)
-    METHODS[:sort] = block
-  end
-
-  def self.sort_by(&block)
-    METHODS[:sort_by] = block
-  end
-
-  def self.html(&block)
-    METHODS[:html] = block
-  end
-
-  def self.filter(&block)
-    METHODS[:filter] = block
-  end
-
-  def self.link(entity, type, params = {}, text = nil, html_class= nil)
-    if entity.nil?
-      ""
-    else
-      text ||= entity
-      "<a class='entity #{ type.sub(/\s/,'_') }#{html_class.nil? ? "" : " " << html_class}' href='#{File.join('/entity', type, entity)}#{
-        if params.nil? or params.empty?
-          ""
-        else
-          "?" + params.collect{|*p| p * "="} * "&"
-        end
-      }'>#{ text }</a>"
-    end
-  end
-
-  def self.define(name, *synonyms, &block)
-    Log.debug "Defining entity #{ name }"
-    Misc.lock(Rbbt.tmp.sinatra_rbbt.find) do
-      self.instance_exec &block
-      ENTITIES[name] = METHODS.dup
-      METHODS.clear
-    end
-    synonyms.each do |syn|
-      SYNONYMS[syn] = name
-    end
-  end
-end
-
 module Entity
+
   module REST
-    def link(text = nil, options = {})
+    LIST_REPO = {}
+
+    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])}
+          self.collect{|e| e.link(translations[e], url, options)}
         else
-          self.collect{|e| e.link(text)}
+          self.collect{|e| e.link(text, url, options)}
         end
       else
+
         text ||= self.name if self.respond_to? :name 
-        text = self if text.nil? or text == :literal
-        klass = self.respond_to?(:format)? self.format : annotation_types.collect{|t| t.to_s} * " "
-        klass += " " << options[:extra_classes] if options.include? :extra_classes
-        type = self.respond_to?(:format)? annotation_types.last.to_s + ":" + self.format : annotation_types.last.to_s
-        annotations_str = self.info.reject{|k,v| [:annotation_types, :format].include? k}.collect{|k,v| [k, CGI.escape(v)] * "="} * "&"
-        "<a class='entity #{klass}' href='#{File.join("/entity", type, self) + '?' + annotations_str}'>#{text}</a>"
+        text = self if text.nil? or text == :literal or text.to_s.strip.empty?
+
+        klass = options[:class]
+        klass ||= "entity " + (self.respond_to?(:format)? 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)? annotation_types.last.to_s + 
+          ":" + 
+          (self.format || "") : annotation_types.last.to_s
+
+        params = options[:params] || self.info.reject{|k,v| [:annotation_types, :format].include?(k)}
+        params.merge! options[:extra_params] if options.include? :extra_params
+
+        url ||= if options.include? :action
+                  File.join("/entity_action", type, options[:action].to_s, self)
+                else
+                  File.join("/entity", type, self)
+                end
+
+        annotations_str = params.collect{|k,v| [k, CGI.escape(v.to_s)] * "="} * "&"
+        "<a class='#{klass}' href='#{url + (annotations_str.any? ? '?' + annotations_str : "")}'>#{text}</a>"
+      end
+    end
+
+    def self.save_list(id, list)
+      Entity::REST::LIST_REPO[id] = list
+    end
+
+    def self.load_list(id)
+      Entity::REST::LIST_REPO[id]
+    end
+
+    def list_link(text = nil, id = nil, options = {})
+      text = self.length if text.nil? or (String === text and text.strip.empty?)
+
+      id ||= options[:id] || Misc.digest((self * "|").inspect)
+
+      Entity::REST.save_list(id, self)
+
+      klass = self.respond_to?(:format)? 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)? annotation_types.last.to_s + ":" + self.format : annotation_types.last.to_s
+
+      annotations_str = self.info.reject{|k,v| [:annotation_types, :format].include?(k)}.collect{|k,v| [k, CGI.escape(v.to_s)] * "="} * "&"
+
+      "<a class='entity_list #{klass}' href='#{File.join("/entity_list", type, id) + (annotations_str.any? ? '?' + annotations_str : "")}'>#{text}</a>"
+    end
+
+    def action_link(action, text = nil, inputs = {})
+      options = inputs.delete(:link_options) || {}
+      clean_inputs = {}
+      inputs.each do |k, v| 
+        clean_inputs[k] = Array === v ? v * "," : v
       end
+      link(text, nil, options.merge(:extra_params => clean_inputs, :action => action))
+    end
+
+    def list_action_link(action, text = nil, id = nil, options = {})
+      text = self.length if text.nil? or (String === text and text.strip.empty?)
+      id ||= options[:id] || Misc.digest((self * "|").inspect)
+
+      text = id if text == :id
+
+      Entity::REST.save_list(id, self)
+
+      klass = self.respond_to?(:format)? 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)? annotation_types.last.to_s + ":" + self.format : annotation_types.last.to_s
+
+      annotations_str = self.info.reject{|k,v| [:annotation_types, :format].include?(k)}.collect{|k,v| [k, CGI.escape(v.to_s)] * "="} * "&"
+
+      "<a class='entity_list_action #{klass}' href='#{File.join("/entity_list_action", type, action, id) + (annotations_str.any? ? '?' + annotations_str : "")}'>#{text}</a>"
     end
+
   end
 end