taverna-player 0.5.0 → 0.6.0

data/config/routes.rb

@@ -31,5 +31,8 @@ TavernaPlayer::Engine.routes.draw do
     end
   end
 
-  resources :service_credentials
+  scope TavernaPlayer.admin_scope do
+    resources :service_credentials
+    get "job_queue", :controller => :job_queue, :action => "index"
+  end
 end

data/db/migrate/20140226135723_change_taverna_player_runs_status_message_to_use_keys.rb

@@ -0,0 +1,19 @@
+class ChangeTavernaPlayerRunsStatusMessageToUseKeys < ActiveRecord::Migration
+  def up
+    rename_column :taverna_player_runs, :status_message, :status_message_key
+
+    TavernaPlayer::Run.all.each do |run|
+      run.status_message_key = run.saved_state
+      run.save
+    end
+  end
+
+  def down
+    rename_column :taverna_player_runs, :status_message_key, :status_message
+
+    TavernaPlayer::Run.all.each do |run|
+      run.status_message = run.saved_state.capitalize
+      run.save
+    end
+  end
+end

data/lib/generators/taverna_player/install_generator.rb

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2013, 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -25,6 +25,11 @@ module TavernaPlayer
           "config/initializers/taverna_server.rb.example"
       end
 
+      def copy_locale
+        copy_file "../../../config/locales/en.yml",
+          "config/locales/taverna_player.en.yml"
+      end
+
       def show_readme
         readme "ReadMe.txt" if behavior == :invoke
       end

data/lib/generators/templates/ReadMe.txt

@@ -23,6 +23,12 @@ Taverna Player configuration, leaving the sensitive parts out.
 In your application's install instructions remember to tell your users to copy
 the example initializer and configure their Taverna Server information.
 
+A locale file has also been installed to:
+
+  config/locales/taverna_player.en.yml
+
+Please edit this to suit your application if required.
+
 There is also some manual setup to do, if you haven't already done it:
 
   1. Mount the Taverna Player engine in your config/routes.rb. For example:

data/lib/generators/templates/controllers/job_queue_controller.rb

@@ -0,0 +1,19 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  class JobQueueController < TavernaPlayer::ApplicationController
+    # Do not remove the next line.
+    include TavernaPlayer::Concerns::Controllers::JobQueueController
+    # Extend the JobQueueControllerController here.
+  end
+end

data/lib/generators/templates/player_initializer.rb

@@ -42,6 +42,14 @@ TavernaPlayer.setup do |config|
   # or use :rails_root for the root directory of your application.
   #config.file_store = ":rails_root/public/system"
 
+  # If you would like to use a different namespace for admin type resources
+  # you can configure it here. Defaults to the empty string.
+  #config.admin_scope = "admin"
+
+  # The queue name for Taverna Player's delayed jobs to be run. Whatever you
+  # use here be sure to start delayed job workers listening to this queue.
+  #config.job_queue_name = "player"
+
   # Callbacks to be run at various points during a workflow run. These can be
   # defined as Proc objects or as methods and referenced by name.
   #

data/lib/tasks/delete-cancelled-runs.rake

@@ -17,7 +17,7 @@ namespace :taverna_player do
     gone = 0
     TavernaPlayer::Run.all.each do |run|
       if run.cancelled?
-        gone += 1 #if run.destroy
+        gone += 1 if run.destroy
       end
     end
 

data/lib/taverna-player.rb

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2013, 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -99,6 +99,10 @@ module TavernaPlayer
   mattr_accessor :file_store
   @@file_store = ":rails_root/public/system"
 
+  # Admin scope for system configuration routes.
+  mattr_accessor :admin_scope
+  @@admin_scope = ""
+
   # Taverna server polling interval (in seconds)
   mattr_accessor :server_poll_interval
   @@server_poll_interval = 5
@@ -111,6 +115,10 @@ module TavernaPlayer
   mattr_accessor :server_connection
   @@server_connection = T2Server::DefaultConnectionParameters.new
 
+  # Queue on which to create workflow execution jobs
+  mattr_accessor :job_queue_name
+  @@job_queue_name = "player"
+
   # Pre run callback
   mattr_accessor :pre_run_callback
   @@pre_run_callback = nil

data/lib/taverna_player/concerns/controllers/job_queue_controller.rb

@@ -0,0 +1,38 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  module Concerns
+    module Controllers
+      module JobQueueController
+
+        extend ActiveSupport::Concern
+
+        included do
+          respond_to :html
+
+          before_filter :find_jobs
+
+          def find_jobs
+            @jobs = Delayed::Job.find_all_by_queue(TavernaPlayer.job_queue_name)
+          end
+        end # included
+
+        # GET job_queue
+        def index
+
+        end
+
+      end
+    end
+  end
+end

data/lib/taverna_player/concerns/controllers/runs_controller.rb

@@ -32,8 +32,6 @@ module TavernaPlayer
           before_filter :filter_update_parameters, :only => :update
           before_filter :find_interaction, :only => [ :read_interaction, :write_interaction ]
 
-          layout :choose_layout
-
           private
 
           def find_runs
@@ -87,15 +85,6 @@ module TavernaPlayer
             send_data @port.value, :type => type, :filename => @port.filename
           end
 
-          # Choose a layout for the page depending on action and embedded status.
-          def choose_layout
-            if (action_name == "new" || action_name == "show") && @run.embedded?
-              "taverna_player/embedded"
-            else
-              ApplicationController.new.send(:_layout).virtual_path
-            end
-          end
-
         end # included
 
         # GET /runs
@@ -119,7 +108,7 @@ module TavernaPlayer
           respond_with(@run) do |format|
             # Render show.{html|js}.erb unless the run is embedded.
             format.any(:html, :js) do
-              render "taverna_player/runs/embedded/show" if @run.embedded
+              render "taverna_player/runs/embedded/show", :layout => "taverna_player/embedded" if @run.embedded
             end
           end
         end
@@ -129,7 +118,7 @@ module TavernaPlayer
           respond_with(@run) do |format|
             # Render new.html.erb unless the run is embedded.
             format.html do
-              render "taverna_player/runs/embedded/new" if @run.embedded
+              render "taverna_player/runs/embedded/new", :layout => "taverna_player/embedded" if @run.embedded
             end
           end
         end

data/lib/taverna_player/concerns/models/run.rb

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2013, 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -20,7 +20,7 @@ module TavernaPlayer
         included do
           attr_accessible :create_time, :delayed_job, :embedded, :finish_time,
             :inputs_attributes, :log, :name, :parent_id, :results, :run_id,
-            :start_time, :status_message, :user_id, :workflow_id
+            :start_time, :status_message_key, :user_id, :workflow_id
 
           # Each run is spawned from a workflow. This provides the link to the
           # workflow model in the parent app, whatever it calls its model.
@@ -48,7 +48,8 @@ module TavernaPlayer
 
           accepts_nested_attributes_for :inputs
 
-          STATES = ["pending", "initialized", "running", "finished", "cancelled", "failed"]
+          STATES = ["pending", "initialized", "running", "finished",
+            "cancelled", "timeout", "failed"]
 
           validates :workflow_id, :presence => true
           validates :name, :presence => true
@@ -65,18 +66,20 @@ module TavernaPlayer
           # needs to be checked on update because on create we don't have an
           # id for ourself.
           validates :parent_id, :numericality => { :less_than => :id,
-              :message => "Parents must have lower ids than children" },
+              :message => I18n.t("taverna_player.errors.invalid-parent") },
             :allow_nil => true, :on => :update
 
           has_attached_file :log,
             :path => File.join(TavernaPlayer.file_store, ":class/:attachment/:id/:filename"),
             :url => "/runs/:id/download/log",
             :default_url => ""
+          do_not_validate_attachment_file_type :log
 
           has_attached_file :results,
             :path => File.join(TavernaPlayer.file_store, ":class/:attachment/:id/:filename"),
             :url => "/runs/:id/download/results",
             :default_url => ""
+          do_not_validate_attachment_file_type :results
 
           after_initialize :initialize_child_run, :if => "new_record? && has_parent?"
           after_create :populate_child_inputs, :if => :has_parent?
@@ -106,8 +109,8 @@ module TavernaPlayer
 
           def enqueue
             worker = TavernaPlayer::Worker.new(self)
-            job = Delayed::Job.enqueue worker, :queue => "player"
-            update_attributes(:delayed_job => job, :status_message => "Queued")
+            job = Delayed::Job.enqueue worker, :queue => TavernaPlayer.job_queue_name
+            update_attributes(:delayed_job => job, :status_message_key => "pending")
           end
 
         end # included
@@ -144,7 +147,7 @@ module TavernaPlayer
               if delayed_job.locked_by.nil?
                 delayed_job.destroy
                 update_attribute(:saved_state, "cancelled")
-                update_attribute(:status_message, "Cancelled")
+                update_attribute(:status_message_key, "cancelled")
               end
             end
           end
@@ -173,6 +176,11 @@ module TavernaPlayer
           self[:saved_state] = s
         end
 
+        def status_message
+          key = status_message_key.nil? ? saved_state : status_message_key
+          I18n.t("taverna_player.status.#{key}")
+        end
+
         def running?
           state == :running
         end
@@ -189,13 +197,18 @@ module TavernaPlayer
           state == :cancelling
         end
 
+        def timeout?
+          state == :timeout
+        end
+
         def failed?
           state == :failed
         end
 
-        # This is used as a catch-all for finished, cancelled and failed
+        # This is used as a catch-all for finished, cancelled, failed and
+        # timeout
         def complete?
-          finished? || cancelled? || failed?
+          finished? || cancelled? || failed? || timeout?
         end
 
         def has_parent?

data/lib/taverna_player/concerns/models/run_port.rb

@@ -37,6 +37,7 @@ module TavernaPlayer
             :path => File.join(TavernaPlayer.file_store, ":class/:attachment/:id/:filename"),
             :url => :file_url_via_run,
             :default_url => ""
+          do_not_validate_attachment_file_type :file
 
           default_scope order("lower(name) ASC")
 
@@ -159,6 +160,10 @@ module TavernaPlayer
           end
         end
 
+        def value=(v)
+          self[:value] = v.force_encoding("BINARY")
+        end
+
         def path(*indices)
           index = [*indices].flatten
           path = index.empty? ? "" : "/" + index.join("/")

data/lib/taverna_player/port_renderer.rb

@@ -53,7 +53,7 @@ module TavernaPlayer
 
       @hash[type.media_type] ||= {}
       @hash[type.media_type][type.sub_type] = method
-      @hash[type.media_type][:default] = method if default
+      type_default(type.media_type, method) if default
     end
 
     # :call-seq:

data/lib/taverna_player/version.rb

@@ -11,5 +11,5 @@
 #------------------------------------------------------------------------------
 
 module TavernaPlayer
-  VERSION = "0.5.0"
+  VERSION = "0.6.0"
 end

data/lib/taverna_player/worker.rb

@@ -15,12 +15,16 @@ module TavernaPlayer
     include TavernaPlayer::Concerns::Callback
     include TavernaPlayer::Concerns::Zip
 
+    attr_reader :run
+
     # How to get the interaction presentation frame out of the interaction page.
     INTERACTION_REGEX = /document\.getElementById\(\'presentationFrame\'\)\.src = \"(.+)\";/
 
-    def initialize(run)
+    # The workflow file to be run can be specified explicitly or it will be
+    # taken from the workflow model.
+    def initialize(run, workflow_file = nil)
       @run = run
-      @workflow = TavernaPlayer.workflow_proxy.class_name.find(@run.workflow_id)
+      @workflow = workflow_file || TavernaPlayer.workflow_proxy.file(@run.workflow)
     end
 
     # This tells delayed_job to only try and complete each run once.
@@ -29,12 +33,9 @@ module TavernaPlayer
     end
 
     def perform
-      unless TavernaPlayer.pre_run_callback.nil?
-        status_message "Running pre-run tasks"
-        callback(TavernaPlayer.pre_run_callback, @run)
-      end
+      return unless run_callback(TavernaPlayer.pre_run_callback, "pre-callback")
 
-      status_message "Connecting to Taverna Server"
+      status_message("connect")
 
       server_uri = URI.parse(TavernaPlayer.server_address)
       credentials = T2Server::HttpBasic.new(TavernaPlayer.server_username,
@@ -43,14 +44,14 @@ module TavernaPlayer
 
       begin
         server = T2Server::Server.new(server_uri, conn_params)
-        wkf = File.read(TavernaPlayer.workflow_proxy.file(@workflow))
+        wkf = File.read(@workflow)
 
         # Try and create the run bearing in mind that the server might be at
         # the limit of runs that it can hold at once.
         begin
           run = server.create_run(wkf, credentials)
         rescue T2Server::ServerAtCapacityError
-          status_message "Server full - please wait; run will start soon"
+          status_message("full")
 
           if cancelled?
             cancel
@@ -61,7 +62,7 @@ module TavernaPlayer
           retry
         end
 
-        status_message "Initializing new workflow run"
+        status_message("initialized")
 
         @run.run_id = run.id
         @run.state = run.status
@@ -69,7 +70,7 @@ module TavernaPlayer
         @run.save
 
         unless @run.inputs.size == 0
-          status_message "Uploading run inputs"
+          status_message("inputs")
           @run.inputs.each do |input|
             unless input.file.blank?
               run.input_port(input.name).file = input.file.path
@@ -84,13 +85,13 @@ module TavernaPlayer
           run.add_password_credential(cred.uri, cred.login, cred.password)
         end
 
-        status_message "Starting run"
+        status_message("start")
         run.name = @run.name
 
         # Try and start the run bearing in mind that the server might be at
         # the limit of runs that it can run at once.
         while !run.start
-          status_message "Server busy - please wait; run will start soon"
+          status_message("busy")
 
           if cancelled?
             cancel(run)
@@ -104,7 +105,7 @@ module TavernaPlayer
         @run.start_time = run.start_time
         @run.save
 
-        status_message "Running"
+        status_message("running")
         until run.finished?
           sleep(TavernaPlayer.server_poll_interval)
           waiting = false
@@ -116,7 +117,7 @@ module TavernaPlayer
 
           run.notifications(:requests).each do |note|
             if @run.has_parent?
-              next if note.has_reply?
+              next if note.has_reply? || note.is_notification?
               int = Interaction.find_by_run_id_and_serial(@run.parent_id, note.serial)
               new_int = Interaction.find_or_initialize_by_run_id_and_serial(@run.id, note.serial)
               if new_int.new_record?
@@ -154,6 +155,10 @@ module TavernaPlayer
                   end
                 end
 
+                if note.is_notification? && !int.new_record?
+                  int.replied = true
+                end
+
                 if int.data.blank?
                   int.data = note.input_data.force_encoding("UTF-8")
                 end
@@ -169,10 +174,10 @@ module TavernaPlayer
             end
           end
 
-          status_message(waiting ? "Waiting for user input" : "Running")
+          status_message(waiting ? "interact" : "running")
         end
 
-        status_message "Gathering run outputs and log"
+        status_message("outputs")
         download_outputs(run)
         download_log(run)
 
@@ -182,41 +187,35 @@ module TavernaPlayer
 
         run.delete
       rescue => exception
-        begin
-          unless run.nil?
-            download_log(run)
-            run.delete
-          end
-        rescue
-          # Try and grab the log then delete the run from Taverna Server here,
-          # but at this point we don't care if we fail...
-        end
-
-        unless TavernaPlayer.run_failed_callback.nil?
-          status_message "Running post-failure tasks"
-          callback(TavernaPlayer.run_failed_callback, @run)
-        end
-
-        backtrace = exception.backtrace.join("\n")
-        @run.failure_message = "#{exception.message}\n#{backtrace}"
-
-        @run.state = :failed
-        @run.finish_time = Time.now
-        status_message "Failed"
+        failed(exception, run)
         return
       end
 
-      unless TavernaPlayer.post_run_callback.nil?
-        status_message "Running post-run tasks"
-        callback(TavernaPlayer.post_run_callback, @run)
-      end
+      return unless run_callback(TavernaPlayer.post_run_callback, "post-callback")
 
       @run.state = :finished
-      status_message "Finished"
+      status_message("finished")
     end
 
     private
 
+    # Run the specified callback and return false on error so that we know to
+    # return out of the worker code completely.
+    def run_callback(cb, message)
+      unless cb.nil?
+        status_message(message)
+        begin
+          callback(cb, @run)
+        rescue => exception
+          failed(exception)
+          return false
+        end
+      end
+
+      # no errors
+      true
+    end
+
     def download_log(run)
       Dir.mktmpdir(run.id, Rails.root.join("tmp")) do |tmp_dir|
         tmp_file_name = File.join(tmp_dir, "log.txt")
@@ -282,8 +281,8 @@ module TavernaPlayer
       File.new(tmp_file)
     end
 
-    def status_message(message)
-      @run.status_message = message
+    def status_message(key)
+      @run.status_message_key = key
       @run.save!
     end
 
@@ -295,21 +294,49 @@ module TavernaPlayer
     end
 
     def cancel(run = nil)
-      status_message "Cancelling"
+      status_message("cancel")
 
       unless run.nil?
         download_log(run)
         run.delete
       end
 
-      unless TavernaPlayer.run_cancelled_callback.nil?
-        status_message "Running post-cancel tasks"
-        callback(TavernaPlayer.run_cancelled_callback, @run)
-      end
+      return unless run_callback(TavernaPlayer.run_cancelled_callback, "cancel-callback")
 
       @run.state = :cancelled
       @run.finish_time = Time.now
-      status_message "Cancelled"
+      status_message("cancelled")
+    end
+
+    def failed(exception, run = nil)
+      begin
+        unless run.nil?
+          download_log(run)
+          run.delete
+        end
+      rescue
+        # Try and grab the log then delete the run from Taverna Server here,
+        # but at this point we don't care if we fail...
+      end
+
+      unless TavernaPlayer.run_failed_callback.nil?
+        status_message("fail-callback")
+
+        begin
+          callback(TavernaPlayer.run_failed_callback, @run)
+        rescue
+          # Again, nothing we can really do here, so...
+        end
+      end
+
+      backtrace = exception.backtrace.join("\n")
+      @run.failure_message = "#{exception.message}\n#{backtrace}"
+
+      @run.finish_time = Time.now
+
+      state = exception.instance_of?(Delayed::WorkerTimeout) ? :timeout : :failed
+      @run.state = state
+      status_message(state.to_s)
     end
 
   end