Merge branch 'master' into list-inputs

* master: (48 commits)
  Update the Changelog.
  Bump version number.
  Factor out the interactions handler in the worker code.
  Document the new connection configuration option.
  [TAV-522] Configure number of network error retries.
  [TAV-522] Handle network level errors (retry).
  Fix the "fail in post run callback" worker test.
  Factor out run creation in the worker.
  Use the latest t2-server client library.
  Update the Changelog.
  Bump version number.
  Use an SVG badge for CodeClimate in the ReadMe.
  Add a routing test for the workflows controller.
  Output JSON for the workflows controller.
  Add specific tests for the ModelProxy class.
  Ensure the proxied models use a rooted (::) namespace.
  Update the ReadMe with new workflow model infomation.
  Set the workflow model proxy more simply.
  Add the internal Workflow stubs to the generators.
  Allow extending of the internal Workflow controller.
  ...

.travis.yml

@@ -3,6 +3,12 @@ rvm:
   - 1.9.3
   - 2.0.0
   - 2.1.2
+  - rbx-2
+  - ruby-head
 script:
   - RAILS_ENV=test bundle exec rake db:schema:load
   - bundle exec rake test
+matrix:
+  allow_failures:
+    - rvm: rbx-2
+    - rvm: ruby-head

CHANGES.rdoc

@@ -1,5 +1,43 @@
 = Changes log for Taverna Player
 
+== Version 0.10.0
+
+* Use the latest t2-server client library.
+* Factor out run creation in the worker.
+* Fix the "fail in post run callback" worker test.
+* [TAV-522] Handle network level errors (retry).
+* [TAV-522] Configure number of network error retries.
+* Document the new connection configuration option.
+* Factor out the interactions handler in the worker code.
+
+== Version 0.9.0
+
+* Add a test to check if a Run's delayed_job has failed.
+* Destroy failed delayed_jobs when destroying Runs.
+* Add a CITATION file.
+* Test cancelling a Run before it starts running.
+* Add Run#pending?
+* Add Run#initialized?
+* Add Run#incomplete?
+* Allow cancelling a run if its delayed_job fails.
+* Add a test for Run#initialized?
+* Use the latest t2flow gem for the tests.
+* Add a default Workflow model.
+* Fix up the user proxy for tests vs the dev app.
+* Update the installer templates.
+* Refactor ModelProxy so constantization is delayed.
+* Set the internal Workflow model to be the default.
+* Only route TavernaPlayer::Workflow if it is in use.
+* Allow extending of the internal Workflow model.
+* Allow extending of the internal Workflow controller.
+* Add the internal Workflow stubs to the generators.
+* Set the workflow model proxy more simply.
+* Update the ReadMe with new workflow model infomation.
+* Ensure the proxied models use a rooted (::) namespace.
+* Add specific tests for the ModelProxy class.
+* Output JSON for the workflows controller.
+* Add a routing test for the workflows controller.
+
 == Version 0.8.0
 
 * Add a note about Taverna Server compatibility to the ReadMe.

CITATION

@@ -0,0 +1,20 @@
+To cite Taverna-Player in your publication please use:
+
+Katherine Wolstencroft, Robert Haines, Donal Fellows, Alan Williams,
+David Withers, Stuart Owen, Stian Soiland-Reyes, Ian Dunlop,
+Aleksandra Nenadic, Paul Fisher, Jiten Bhagat, Khalid Belhajjame, Finn Bacall,
+Alex Hardisty, Abraham Nieva de la Hidalga, Maria P Balcazar Vargas,
+Shoaib Sufi, Carole Goble. The Taverna workflow suite: designing and
+executing workflows of Web Services on the desktop, web or in the cloud in
+Nucleic acids research, 2013, Volume 41, Issue W1, pp W557-W561.
+
+@article{wolstencroft2013taverna,
+  title={The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud},
+  author={Wolstencroft, Katherine and Haines, Robert and Fellows, Donal and Williams, Alan and Withers, David and Owen, Stuart and Soiland-Reyes, Stian and Dunlop, Ian and Nenadic, Aleksandra and Fisher, Paul and others},
+  journal={Nucleic acids research},
+  volume={41},
+  number={W1},
+  pages={W557--W561},
+  year={2013},
+  publisher={Oxford University Press}
+}

Gemfile

@@ -1,18 +1,6 @@
 source "https://rubygems.org"
 
-# Declare your gem's dependencies in taverna_player.gemspec.
-# Bundler will treat runtime dependencies like base dependencies, and
-# development dependencies will be added by default to the :development group.
 gemspec
 
 # These gems are used by the dummy application
 gem "jquery-rails"
-gem "taverna-t2flow", "~> 0.4.5"
-
-# Declare any dependencies that are still in development here instead of in
-# your gemspec. These might include edge Rails or gems from your path or
-# Git. Remember to move these dependencies to your gemspec before releasing
-# your gem to rubygems.org.
-
-# To use debugger
-# gem 'debugger'

README.rdoc

@@ -7,7 +7,7 @@ Licence::     BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license
 Copyright::   (c) 2013, 2014 The University of Manchester, UK
 
 {<img src="https://badge.fury.io/rb/taverna-player.svg" 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://codeclimate.com/github/myGrid/taverna-player/badges/gpa.svg" />}[https://codeclimate.com/github/myGrid/taverna-player]
 {<img src="https://travis-ci.org/myGrid/taverna-player.svg?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]
 
@@ -22,9 +22,8 @@ Taverna Player handles all aspects of running a workflow including:
 * Presenting workflow interactions to the user
 * Gathering and download of workflow outputs
 
-It, purposefully, does not:
-* Manage workflows
-* Manage users
+It, purposefully, does not manage users and its default workflow model is
+intentionally oversimplified.
 
 == Prerequisites
 
@@ -109,9 +108,10 @@ 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:
+Taverna Player provides four resources with paths:
 
 * <tt>/runs/*</tt>
+* <tt>/workflows/*</tt>
 * <tt>/service_credentials/*</tt>
 * <tt>/job_queue</tt>
 
@@ -129,11 +129,18 @@ set (for example):
 And the resource paths would become:
 
 * <tt>/runs/*</tt>
+* <tt>/workflows/*</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:
+The supplied workflow model also nests the run resources within it:
+
+* <tt>/workflows</tt>
+* <tt>/workflows/{workflow-id}/runs/*</tt>
+
+If you override the default workflow model (see below for details) you can
+also nest the Taverna Player runs resources within your workflows resources if
+you wish, like this (within your application's <tt>config/routes.rb</tt>):
 
   resources :workflows do
     resources :runs, :controller => "TavernaPlayer::Runs", :except => :edit
@@ -198,13 +205,13 @@ so that they take precedence over the default ones. You can delete any that you
 do not need to customize but there are no penalties for leaving them there.
 There is more information on overriding controllers below.
 
-If you need to override the Taverna Player Run model, to add columns to the
-table for example, you can copy a customizable stub with:
+If you need to override any Taverna Player models, to add columns to a table
+for example, you can copy customizable stubs with:
 
   rails generate taverna_player:models
 
-The stub is copied to the <tt>app/models/taverna_player</tt> directory so that
-it takes precedence over the default one. There is more information on
+The stubs are copied to the <tt>app/models/taverna_player</tt> directory so
+that they take precedence over the defaults. There is more information on
 overriding models below.
 
 If you want to use pre- and post-run callbacks you can setup some basic stubs
@@ -229,16 +236,17 @@ information on renderers below.
 == Taverna Player initializers
 
 Two initializers are installed by the install generator:
-* {taverna_player.rb}[https://github.com/myGrid/taverna-player/blob/master/lib/generators/templates/player_initializer.rb]:
+* {config/initializers/taverna_player.rb}[https://github.com/myGrid/taverna-player/blob/master/lib/generators/templates/player_initializer.rb]:
   This contains configuration of Taverna Player.
-* {taverna_server.rb.example}[https://github.com/myGrid/taverna-player/blob/master/lib/generators/templates/server_initializer.rb]:
+* {config/initializers/taverna_server.rb.example}[https://github.com/myGrid/taverna-player/blob/master/lib/generators/templates/server_initializer.rb]:
   This is used to configure Taverna Player's connection to a Taverna Server.
   It is initially set up as an example file as you will need to distribute
   this with your application but you must not check in the contents of the
   configured version to your repository.
 
-Both of these files require minimal configuration for simple set ups and are
-fully commented with everything that needs to be set - more details below.
+Both of these files <b>require minimal configuration</b> for simple set ups
+and are fully commented with everything that needs to be set - more details
+below.
 
 === Essential (required) configuration
 
@@ -252,6 +260,10 @@ called "file_name" then the following will configure this correctly:
     proxy.file_method_name = :file_name
   end
 
+Taverna Player has a very simple internal workflow model
+(TavernaPlayer::Workflow) that you can extend (see below) or replace with the
+above code.
+
 Secondly, Taverna Player needs to know where your Taverna Server is and how to
 authenticate to it:
 
@@ -301,7 +313,19 @@ that make use of interactions (so you have users watching the workflows
 running) then it should probably be set lower.
 
 There are a number of options for configuring the connection to the Taverna
-Server. These are actually provided by the underlying
+Server. The first specifies how many times an initial connection to Taverna
+Server will be retried if there are any low level network errors.
+
+  config.server_connection_error_retries = 5
+
+These can be events such as timeouts, broken connections, refused connections
+or anything else out of our control. If such an error is detected Taverna
+Player will back off for the amount of time specified by
+<tt>config.server_retry_interval</tt> before retrying. If the maximum number of
+retries is reached and there is still an error then the run will fail; the
+network error message will be recorded as the reason for the run's failure.
+
+The rest of the connection options are actually provided by the underlying
 {t2-server client library}[https://rubygems.org/gems/t2-server] and surfaced
 here for extra control. They are
 {documented in more detail}[http://mygrid.github.io/t2-server-gem/] elsewhere
@@ -395,7 +419,9 @@ You can override the following core components:
 * RunPort (model)
 * RunPort::Input (model)
 * RunPort::Output (model)
+* Workflow (model)
 * RunsController
+* WorkflowController
 * ServiceCredentialsController
 * JobQueueController
 
@@ -466,7 +492,7 @@ An example callback that just prints out the run's name and workflow id would
 be:
 
   def player_run_callback(run)
-    w = Workflow.find(run.workflow_id)
+    w = TavernaPlayer::Workflow.find(run.workflow_id)
     puts "Callback called for run '#{run.name}' of workflow '#{w.id}'"
   end
 

Rakefile

@@ -39,6 +39,7 @@ RDoc::Task.new(:rdoc) do |rdoc|
     "app/models/taverna_player/run.rb",
     "app/models/taverna_player/run_port.rb",
     "app/models/taverna_player/service_credential.rb",
+    "app/models/taverna_player/workflow.rb",
     "lib/taverna-player.rb",
     "lib/taverna_player/port_renderer.rb"
     ]

app/controllers/taverna_player/workflows_controller.rb

@@ -0,0 +1,18 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2013, 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 WorkflowsController < TavernaPlayer::ApplicationController
+    # See lib/taverna_player/concerns/controllers/workflows_controller.rb
+    include TavernaPlayer::Concerns::Controllers::WorkflowsController
+  end
+end

app/helpers/taverna_player/application_helper.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.
 #
@@ -44,7 +44,7 @@ def workflow_id(id_or_model)
       case id_or_model
       when TavernaPlayer::Run
         id_or_model.workflow_id
-      when TavernaPlayer.workflow_proxy.class_name
+      when TavernaPlayer.workflow_proxy.class_const
         id_or_model.id
       else
         id_or_model

app/models/taverna_player/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.
 #
@@ -36,8 +36,9 @@ class Run < ActiveRecord::Base
     # :call-seq:
     #   complete? -> boolean
     #
-    # Is this run complete? If a run is finished or cancelled or failed or
-    # has timed out then it is complete.
+    # Is this run complete? If a run is finished or cancelled or failed or its
+    # underlying worker has failed or it has timed out then it is complete.
+    # #complete? is not quite the direct opposite of #incomplete?
 
     ##
     # :method: embedded?
@@ -76,13 +77,44 @@ class Run < ActiveRecord::Base
     #
     # A run will have a parent if it is a child run as part of a sweep.
 
+    ##
+    # :method: incomplete?
+    # :call-seq:
+    #   incomplete? -> boolean
+    #
+    # Is this run incomplete? If a run is pending or initialized or running
+    # then it is incomplete. #incomplete? is not quite the direct opposite of
+    # #complete?
+
+    ##
+    # :method: initialized?
+    # :call-seq:
+    #   initialized? -> boolean
+    #
+    # Is this run initialized on Taverna Server but not running yet?
+
+    ##
+    # :method: job_failed?
+    # :call-seq:
+    #   job_failed? -> boolean
+    #
+    # Did the delayed_job worker running this run fail? This is primarily
+    # intended for internal use only at the moment.
+
     ##
     # :method: name
     # :call-seq:
     #   name -> string
     #
     # The name (mnemonic) of this run.
 
+    ##
+    # :method: pending?
+    # :call-seq:
+    #   pending? -> boolean
+    #
+    # Is this run in the queue?
+
     ##
     # :method: root_ancestor
     # :call-seq:

app/models/taverna_player/workflow.rb

@@ -0,0 +1,41 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2013, 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
+
+  # This class represents a workflow. It is provided as an example model and
+  # can be extended or replaced as required.
+  #
+  # To replace the model completely please read about configuring the workflow
+  # model proxy in the "Taverna Player initializers" section of the ReadMe. To
+  # extend the model please read about "Overriding the default models and
+  # controllers" in the ReadMe.
+  class Workflow < ActiveRecord::Base
+    include TavernaPlayer::Concerns::Models::Workflow
+
+    ##
+    # :method: inputs
+    # :call-seq:
+    #   inputs -> Hash
+    #
+    # Return a hash of information about this workflow's inputs. The fields
+    # provided are:
+    # * <tt>:name</tt> - The name of the input port.
+    # * <tt>:description</tt> - A textual description (if provided) of the
+    #   input port.
+    # * <tt>:example</tt> - Example input data (if provided) for the input
+    #   port.
+    #
+    # All data is read directly from the workflow file itself.
+
+  end
+end

app/views/taverna_player/workflows/_info.json.jbuilder

@@ -0,0 +1 @@
+json.extract! workflow, :id, :title, :author, :description

test/dummy/app/views/workflows/index.html.erb → app/views/taverna_player/workflows/index.html.erb

@@ -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.
   #