taverna-player 0.5.0 → 0.6.0

data/.gitignore

@@ -11,6 +11,7 @@ test/dummy/config/initializers/taverna_server.rb
 
 *~
 rdoc/
+coverage/
 .buildpath
 .project
 .settings

data/.travis.yml

@@ -0,0 +1,8 @@
+language: ruby
+rvm:
+  - 1.9.3
+  - 2.0.0
+  - 2.1.0
+script:
+  - RAILS_ENV=test bundle exec rake db:schema:load
+  - bundle exec rake test

data/CHANGES.rdoc

@@ -1,5 +1,52 @@
 = Changes log for Taverna Player
 
+== Version 0.6.0
+
+* [TAV-485] Set up separate worker integration test.
+* [TAV-469] Fix notification interactions.
+* Delete cancelled runs rake task not working.
+* [TAV-495] Stop interactions from changing the document title.
+* [TAV-493] Namespace preset values for embedded runs.
+* Setup Travis-CI.
+* Add a travis badge to the readme.
+* Add Coveralls integration to the tests.
+* Allow configuration of the delayed_job queue name.
+* Update tests to properly test all callback code.
+* Add documentation for the job_queue_name option.
+* [TAV-496] Allow workflow file to be passed in to worker.
+* Guard against missing input presets in embedded view.
+* Add a job queue listing page.
+* Move admin type resources into their own namespace.
+* [TAV-485] Better tests for the worker code.
+* [TAV-485] Ensure run is backed-off before starting.
+* [TAV-485] Ensure run is backed-off before creation.
+* [TAV-485] Test a failing run.
+* [TAV-485] Test a cancelled run.
+* Add a coveralls badge to the readme.
+* Factor out the worker failure handler.
+* Add a worker test for failure within the failure callback.
+* Add a worker test for failure within the cancelled callback.
+* Assert that there is a run failure message on failure.
+* Add a worker test for failure within the pre_run callback.
+* Add a worker test for failure within the post_run callback.
+* [TAV-457] Add I18n file for run status messages.
+* [TAV-457] Install the locale file in the install generator.
+* Don't save translated run status message in the database.
+* Use the locale file for validation error message.
+* [TAV-499] Clean up timed out runs properly.
+* Update missed translation keys in the installed locale file.
+* Update the coderay dependency.
+* Update the delayed_job dependency.
+* Update Paperclip dependency.
+* Update the JBuilder dependency.
+* Allow use of latest jquery-rails gem.
+* Factor out running callbacks in the worker.
+* Simplified method of choosing which layout to use
+* Force input data to be treated as binary initially.
+* Add tests for small non-ascii/utf-8 values.
+* Make the controller dependency chain more explicit.
+* Added test to see if input RunPorts are created along with the run
+
 == Version 0.5.0
 
 * [TAV-480] Refactor output port downloading.

data/README.rdoc

@@ -8,6 +8,8 @@ Copyright::   (c) 2013, 2014 The University of Manchester, UK
 
 {<img src="https://badge.fury.io/rb/taverna-player.png" alt="Gem Version" />}[http://badge.fury.io/rb/taverna-player]
 {<img src="https://codeclimate.com/github/myGrid/taverna-player.png" />}[https://codeclimate.com/github/myGrid/taverna-player]
+{<img src="https://travis-ci.org/myGrid/taverna-player.png?branch=master" alt="Build Status" />}[https://travis-ci.org/myGrid/taverna-player]
+{<img src="https://coveralls.io/repos/myGrid/taverna-player/badge.png?branch=master" alt="Coverage Status" />}[https://coveralls.io/r/myGrid/taverna-player?branch=master]
 
 == Synopsis
 
@@ -41,9 +43,10 @@ Next you need to run the install generator:
 This installs two initializer files (into your application's
 <tt>config/initializers</tt> directory) which describe all of Taverna Player's
 configuration options; there are some things that MUST be configured before it
-will work - see below for more information. The install generator also prints
-out a list of other steps for setting up Taverna Player; these are repeated
-and detailed below.
+will work - see below for more information. The install generator also creates
+a locale file at <tt>config/locales/taverna_player.en.yml</tt> and prints out
+a list of other steps for setting up Taverna Player; these are repeated and
+detailed below.
 
 == Running Taverna Player
 
@@ -79,6 +82,10 @@ would start your workers like this:
 
   RAILS_ENV=production bundle exec ./script/delayed_job -n 20 --queue=player start
 
+By default Taverna Player puts its jobs into the "player" queue which is why
+this is specified above. If you change this configuration (see below) you will
+need to specify a different queue in the command above.
+
 See the documentation for {delayed_job}[https://rubygems.org/gems/delayed_job]
 for more options and information.
 
@@ -88,6 +95,29 @@ Mount the Taverna Player engine in your <tt>config/routes.rb</tt>. For example:
 
   mount TavernaPlayer::Engine, :at => "/"
 
+Taverna Player provides three resources with paths:
+
+* <tt>/runs/*</tt>
+* <tt>/service_credentials/*</tt>
+* <tt>/job_queue</tt>
+
+Runs are what you will interact with most as this is the model that represents
+a workflow execution.
+
+Service credentials and the job queue are administrator resources. If you have
+users you may like to restrict access to these resources (see the section on
+overriding controllers, below). These two resources can be moved to a
+different namespace if you like. In the Taverna Player initializer you can
+set (for example):
+
+  config.admin_scope = "admin"
+
+And the resource paths would become:
+
+* <tt>/runs/*</tt>
+* <tt>/admin/service_credentials/*</tt>
+* <tt>/admin/job_queue</tt>
+
 You can also nest the Taverna Player runs resources within your workflows
 resources if you wish, like this:
 
@@ -317,6 +347,15 @@ want it to store its files:
 Use ":rails_root" for the root of your application, or specify a full path for
 anywhere else.
 
+==== Jobs
+
+Taverna Player uses the "player" queue for its delayed jobs. You can change
+this with:
+
+  config.job_queue_name = "my_queue"
+
+Remember to start workers listening to the correct queue if you change it.
+
 ==== Run callbacks and renderers
 
 These are described in their own sections, below.
@@ -344,6 +383,7 @@ You can override the following core components:
 * RunPort::Output (model)
 * RunsController
 * ServiceCredentialsController
+* JobQueueController
 
 Use the generators, detailed above, to create stubs for you to expand. These
 components have been designed for overriding with the decorator pattern using

data/Rakefile

@@ -1,6 +1,6 @@
 #!/usr/bin/env rake
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2013, 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -49,8 +49,6 @@ end
 APP_RAKEFILE = File.expand_path("../test/dummy/Rakefile", __FILE__)
 load 'rails/tasks/engine.rake'
 
-
-
 Bundler::GemHelper.install_tasks
 
 require 'rake/testtask'
@@ -62,5 +60,4 @@ Rake::TestTask.new(:test) do |t|
   t.verbose = false
 end
 
-
 task :default => :test

data/app/assets/stylesheets/taverna_player/coderay.css

@@ -13,7 +13,7 @@ table.CodeRay { border-collapse: collapse; width: 100%; padding: 2px; }
 table.CodeRay td { padding: 2px 4px; vertical-align: top; }
 
 .CodeRay .line-numbers {
-  background-color: hsl(100,65%,90%);
+  background-color: hsl(180,65%,90%);
   color: gray;
   text-align: right;
   -webkit-user-select: none;
@@ -21,10 +21,13 @@ table.CodeRay td { padding: 2px 4px; vertical-align: top; }
   user-select: none;
 }
 .CodeRay .line-numbers a {
-  background-color: hsl(100,65%,90%) !important;
+  background-color: hsl(180,65%,90%) !important;
   color: gray !important;
   text-decoration: none !important;
 }
+.CodeRay .line-numbers pre {
+  word-break: normal;
+}
 .CodeRay .line-numbers a:target { color: blue !important; }
 .CodeRay .line-numbers .highlighted { color: red !important; }
 .CodeRay .line-numbers .highlighted a { color: red !important; }
@@ -37,77 +40,84 @@ table.CodeRay td { padding: 2px 4px; vertical-align: top; }
 .CodeRay .annotation { color:#007 }
 .CodeRay .attribute-name { color:#b48 }
 .CodeRay .attribute-value { color:#700 }
-.CodeRay .binary { color:#509 }
+.CodeRay .binary { color:#549 }
+.CodeRay .binary .char { color:#325 }
+.CodeRay .binary .delimiter { color:#325 }
+.CodeRay .char { color:#D20 }
 .CodeRay .char .content { color:#D20 }
 .CodeRay .char .delimiter { color:#710 }
-.CodeRay .char { color:#D20 }
 .CodeRay .class { color:#B06; font-weight:bold }
 .CodeRay .class-variable { color:#369 }
 .CodeRay .color { color:#0A0 }
 .CodeRay .comment { color:#777 }
 .CodeRay .comment .char { color:#444 }
 .CodeRay .comment .delimiter { color:#444 }
-.CodeRay .complex { color:#A08 }
 .CodeRay .constant { color:#036; font-weight:bold }
 .CodeRay .decorator { color:#B0B }
 .CodeRay .definition { color:#099; font-weight:bold }
 .CodeRay .delimiter { color:black }
 .CodeRay .directive { color:#088; font-weight:bold }
-.CodeRay .doc { color:#970 }
-.CodeRay .doc-string { color:#D42; font-weight:bold }
+.CodeRay .docstring { color:#D42; }
 .CodeRay .doctype { color:#34b }
+.CodeRay .done { text-decoration: line-through; color: gray }
 .CodeRay .entity { color:#800; font-weight:bold }
 .CodeRay .error { color:#F00; background-color:#FAA }
 .CodeRay .escape  { color:#666 }
 .CodeRay .exception { color:#C00; font-weight:bold }
 .CodeRay .float { color:#60E }
 .CodeRay .function { color:#06B; font-weight:bold }
+.CodeRay .function .delimiter { color:#024; font-weight:bold }
 .CodeRay .global-variable { color:#d70 }
 .CodeRay .hex { color:#02b }
-.CodeRay .imaginary { color:#f00 }
+.CodeRay .id  { color:#33D; font-weight:bold }
 .CodeRay .include { color:#B44; font-weight:bold }
 .CodeRay .inline { background-color: hsla(0,0%,0%,0.07); color: black }
 .CodeRay .inline-delimiter { font-weight: bold; color: #666 }
 .CodeRay .instance-variable { color:#33B }
 .CodeRay .integer  { color:#00D }
+.CodeRay .imaginary { color:#f00 }
+.CodeRay .important { color:#D00 }
+.CodeRay .key { color: #606 }
 .CodeRay .key .char { color: #60f }
 .CodeRay .key .delimiter { color: #404 }
-.CodeRay .key { color: #606 }
 .CodeRay .keyword { color:#080; font-weight:bold }
 .CodeRay .label { color:#970; font-weight:bold }
-.CodeRay .local-variable { color:#963 }
+.CodeRay .local-variable { color:#950 }
+.CodeRay .map .content { color:#808 }
+.CodeRay .map .delimiter { color:#40A}
+.CodeRay .map { background-color:hsla(200,100%,50%,0.06); }
 .CodeRay .namespace { color:#707; font-weight:bold }
 .CodeRay .octal { color:#40E }
 .CodeRay .operator { }
 .CodeRay .predefined { color:#369; font-weight:bold }
 .CodeRay .predefined-constant { color:#069 }
-.CodeRay .predefined-type { color:#0a5; font-weight:bold }
+.CodeRay .predefined-type { color:#0a8; font-weight:bold }
 .CodeRay .preprocessor { color:#579 }
 .CodeRay .pseudo-class { color:#00C; font-weight:bold }
+.CodeRay .regexp { background-color:hsla(300,100%,50%,0.06); }
 .CodeRay .regexp .content { color:#808 }
 .CodeRay .regexp .delimiter { color:#404 }
 .CodeRay .regexp .modifier { color:#C2C }
-.CodeRay .regexp { background-color:hsla(300,100%,50%,0.06); }
 .CodeRay .reserved { color:#080; font-weight:bold }
+.CodeRay .shell { background-color:hsla(120,100%,50%,0.06); }
 .CodeRay .shell .content { color:#2B2 }
 .CodeRay .shell .delimiter { color:#161 }
-.CodeRay .shell { background-color:hsla(120,100%,50%,0.06); }
+.CodeRay .string { background-color:hsla(0,100%,50%,0.05); }
 .CodeRay .string .char { color: #b0b }
 .CodeRay .string .content { color: #D20 }
 .CodeRay .string .delimiter { color: #710 }
 .CodeRay .string .modifier { color: #E40 }
-.CodeRay .string { background-color:hsla(0,100%,50%,0.05); }
-.CodeRay .symbol .content { color:#A60 }
-.CodeRay .symbol .delimiter { color:#630 }
 .CodeRay .symbol { color:#A60 }
-.CodeRay .tag { color:#070 }
+.CodeRay .symbol .content { color:#A60 }
+.CodeRay .symbol .delimiter { color:#740 }
+.CodeRay .tag { color:#070; font-weight:bold }
 .CodeRay .type { color:#339; font-weight:bold }
-.CodeRay .value { color: #088; }
-.CodeRay .variable  { color:#037 }
+.CodeRay .value { color: #088 }
+.CodeRay .variable { color:#037 }
 
 .CodeRay .insert { background: hsla(120,100%,50%,0.12) }
 .CodeRay .delete { background: hsla(0,100%,50%,0.12) }
-.CodeRay .change { color: #bbf; background: #007; }
+.CodeRay .change { color: #bbf; background: #007 }
 .CodeRay .head { color: #f8f; background: #505 }
 .CodeRay .head .filename { color: white; }
 

data/app/controllers/taverna_player/application_controller.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.
 #
@@ -11,6 +11,6 @@
 #------------------------------------------------------------------------------
 
 module TavernaPlayer
-  class ApplicationController < ApplicationController
+  class ApplicationController < ::ApplicationController
   end
 end

data/app/controllers/taverna_player/job_queue_controller.rb

@@ -0,0 +1,18 @@
+#------------------------------------------------------------------------------
+# 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
+    # See lib/taverna_player/concerns/controllers/job_queue_controller.rb
+    include TavernaPlayer::Concerns::Controllers::JobQueueController
+  end
+end

data/app/models/taverna_player/run.rb

@@ -36,8 +36,8 @@ module TavernaPlayer
     # :call-seq:
     #   complete? -> boolean
     #
-    # Is this run complete? If a run is finished or cancelled or failed then
-    # it is complete.
+    # Is this run complete? If a run is finished or cancelled or failed or
+    # has timed out then it is complete.
 
     ##
     # :method: embedded?
@@ -111,7 +111,14 @@ module TavernaPlayer
     #   state -> symbol
     #
     # The state of this run. Possible states are :pending, :initialized,
-    # :running, :finished, :cancelled or :failed.
+    # :running, :finished, :cancelled, :timeout or :failed.
+
+    ##
+    # :method: timeout?
+    # :call-seq:
+    #   timeout? -> boolean
+    #
+    # Did this run timeout?
 
   end
 end

data/app/views/taverna_player/job_queue/index.html.erb

@@ -0,0 +1,47 @@
+<%
+  # 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
+%>
+
+<h1>Taverna Player Jobs</h1>
+
+Number of jobs in the queue: <%= @jobs.count %>
+
+<table>
+  <tr>
+    <th>Job ID</th>
+    <th>Priority</th>
+    <th>Run at</th>
+    <th>Locked at</th>
+    <th>Failed at</th>
+    <th>Run ID</th>
+    <th>Workflow ID</th>
+    <th>Run state</th>
+    <th>Status message</th>
+  </tr>
+
+<% @jobs.each do |job| %>
+  <%
+    worker = job.payload_object
+    run = worker.run
+  %>
+  <tr>
+    <td><%= job.id %></td>
+    <td><%= job.priority %></td>
+    <td><%= job.run_at %></td>
+    <td><%= job.locked_at %></td>
+    <td><%= job.failed_at %></td>
+    <td><%= run.id %></td>
+    <td><%= run.workflow.id %></td>
+    <td><%= run.state %></td>
+    <td><%= run.status_message %></td>
+  </tr>
+<% end %>
+</table>

data/app/views/taverna_player/runs/_interaction.html.erb

@@ -49,7 +49,13 @@
       pmrpc.register( {
         publicProcedureName : "setTitle",
         procedure : function(title) {
-          document.title = title;
+          // This method is called by an interaction to set its title.
+          // It must be registered but doesn't need to do anything if you
+          // don't want it to.
+
+          //document.title = title;
+
+          // This method must return "OK".
           return "OK";
         }
       });

data/app/views/taverna_player/runs/embedded/new.html.erb

@@ -21,7 +21,7 @@
   <%= f.hidden_field :name, :value => "#{workflow_title} (embedded)" %>
 
   <% workflow_inputs.each do |input| %>
-    <% input_param = params[input[:name].to_sym] %>
+    <% input_param = params[:input][input[:name].to_sym] if params[:input] %>
     <% if input_param.nil? %>
       <div>Input: <%= input[:name] %></div>
 

data/config/locales/en.yml

@@ -0,0 +1,36 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+en:
+  taverna_player:
+    status:
+      pending: "Queued"
+      pre-callback: "Running pre-run tasks"
+      connect: "Connecting to Taverna Server"
+      full: "Server full - please wait; run will start soon"
+      initialized: "Initializing new workflow run"
+      inputs: "Uploading run inputs"
+      start: "Starting run"
+      busy: "Server busy - please wait; run will start soon"
+      running: "Running"
+      interact: "Waiting for user input"
+      outputs: "Gathering run outputs and log"
+      post-callback: "Running post-run tasks"
+      finished: "Finished"
+      cancel: "Cancelling"
+      cancel-callback: "Running post-cancel tasks"
+      cancelled: "Cancelled"
+      timeout: "Run execution timed out"
+      fail-callback: "Running post-failure tasks"
+      failed: "Failed"
+    errors:
+      invalid-parent: "Parents must have lower ids than their children"