taverna-player 0.1.0

data/app/views/taverna_player/runs/index.json.jbuilder

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+json.array! @runs, :partial => "info", :as => :run

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

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+<%
+  # Copyright (c) 2013 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
+%>
+
+<% workflow_title = TavernaPlayer.workflow_proxy.title(@workflow) || "" %>
+<% workflow_inputs = TavernaPlayer.workflow_proxy.inputs(@workflow) %>
+
+<h1>Workflow: &quot;<%= workflow_title %>&quot;</h1>
+<h2>Set inputs</h2>
+
+<%= form_for @run, :html => {:multipart => true} do |f| %>
+  <%= f.hidden_field :workflow_id %>
+  <%= f.hidden_field :embedded %>
+
+  <div>
+    <%= f.label :name, "Run name:" %>
+    <%= f.text_field :name, :value => workflow_title %>
+  </div>
+
+  <% workflow_inputs.each do |input| %>
+    <div>Input: <%= input[:name] %></div>
+
+    <% unless input[:description].blank? %>
+      <div>Description: <%= input[:description] %></div>
+    <% end %>
+
+    <% unless input[:example].blank? %>
+      <div>Example value: <%= input[:example] %></div>
+      <div>
+        The example value is automatically entered in the box below.
+        Click to edit or enter a new value directly or choose a file.
+      </div>
+    <% else %>
+      <div>Set this input by entering data directly or choosing a file.</div>
+    <% end %>
+
+    <%= f.fields_for :inputs, TavernaPlayer::RunPort::Input.new do |input_fields| %>
+      <%= input_fields.hidden_field :name, :value => input[:name] %>
+      <%= input_fields.text_area :value, :value => input[:example], :rows => 3 %>
+      <%= input_fields.file_field :file %>
+    <% end %>
+  <% end %>
+
+  <div><%= f.submit 'Start Run' %></div>
+<% end %>
+<% unless @run.embedded? %>
+  <%= link_to 'Cancel', :back %>
+<% end %>

data/app/views/taverna_player/runs/new.json.jbuilder

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+json.partial! "info", :run => @run

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

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+<%
+  # Copyright (c) 2013 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>Run</h1>
+
+<%= render "info", :run => @run %>
+
+<%= render "button", :run => @run %>
+
+<% if @run.inputs.size > 0 %>
+  <%= render "inputs", :run => @run %>
+<% end %>
+
+<%= render "interaction", :run => @run, :interaction => @interaction %>
+
+<%= render "outputs", :run => @run %>
+
+<% unless @run.complete? %>
+  <%= render "poll", :reload => run_path(@run) %>
+<% end %>

data/app/views/taverna_player/runs/show.js.erb

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+<%
+  # Copyright (c) 2013 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
+%>
+
+jQuery("#run-info").replaceWith('<%= escape_javascript(render("info", :run => @run)) %>');
+
+jQuery("#run-button").replaceWith('<%= escape_javascript(render("button", :run => @run)) %>');
+
+<% if @interaction.nil? || @new_interaction %>
+  jQuery("#run-interaction").replaceWith('<%= escape_javascript(render("interaction", :run => @run, :interaction => @interaction)) %>');
+<% end %>
+
+<% if @run.complete? %>
+  jQuery("#run-outputs").replaceWith('<%= escape_javascript(render("outputs", :run => @run)) %>');
+<% else %>
+  jQuery("#run-poll").replaceWith('<%= escape_javascript(render("poll", :reload => run_path(@run))) %>');
+<% end %>

data/app/views/taverna_player/runs/show.json.jbuilder

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+json.partial! "info", :run => @run
+
+json.partial! "inputs", :inputs => @run.inputs
+
+if @run.outputs.size > 0
+  json.outputs @run.outputs do |output|
+    json.name output.name
+    json.depth output.depth
+    json.uri run_path(@run) + "/output/#{output.name}"
+  end
+
+  json.outputs_zip @run.results.url
+end
+
+unless @run.log.blank?
+  json.log @run.log.url
+end
+
+unless @interaction.nil?
+  json.interaction do
+    json.id @interaction.unique_id
+    json.serial @interaction.serial
+    json.uri interaction_redirect(@interaction)
+  end
+end

data/app/views/taverna_player/service_credentials/_form.html.erb

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+<%
+  # Copyright (c) 2013 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
+%>
+
+<%= form_for(service_credential) do |f| %>
+  <% if service_credential.errors.any? %>
+    <div id="error_explanation">
+      <h2><%= pluralize(service_credential.errors.count, "error") %> prohibited this service_credential from being saved:</h2>
+
+      <ul>
+      <% service_credential.errors.full_messages.each do |msg| %>
+        <li><%= msg %></li>
+      <% end %>
+      </ul>
+    </div>
+  <% end %>
+
+  <div class="field">
+    <%= f.label :name %><br />
+    <%= f.text_field :name %>
+  </div>
+  <div class="field">
+    <%= f.label :description %><br />
+    <%= f.text_area :description %>
+  </div>
+    <div class="field">
+    <%= f.label :uri, "URI" %><br />
+    <%= f.text_field :uri %>
+  </div>
+  <div class="field">
+    <%= f.label :login %><br />
+    <%= f.text_field :login %>
+  </div>
+  <div class="field">
+    <%= f.label :password %><br />
+    <%= f.password_field :password %>
+  </div>
+  <div class="field">
+    <%= f.label :password_confirmation %><br />
+    <%= f.password_field :password_confirmation %>
+  </div>
+  <div class="actions">
+    <%= f.submit %>
+  </div>
+<% end %>

data/app/views/taverna_player/service_credentials/edit.html.erb

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+<%
+  # Copyright (c) 2013 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>Editing service_credential</h1>
+
+<%= render 'form', :service_credential => @service_credential %>
+
+<%= link_to 'Show', @service_credential %> |
+<%= link_to 'Back', service_credentials_path %>

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

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+<%
+  # Copyright (c) 2013 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>Listing Service Credentials</h1>
+
+<table>
+  <tr>
+    <th>Name</th>
+    <th>Description</th>
+    <th>URI</th>
+    <th>Login</th>
+    <th></th>
+    <th></th>
+    <th></th>
+  </tr>
+
+<% @service_credentials.each do |service_credential| %>
+  <tr>
+    <td><%= service_credential.name %></td>
+    <td><%= service_credential.description %></td>
+    <td><%= service_credential.uri %></td>
+    <td><%= service_credential.login %></td>
+    <td><%= link_to 'Show', service_credential %></td>
+    <td><%= link_to 'Edit', edit_service_credential_path(service_credential) %></td>
+    <td><%= link_to 'Destroy', service_credential, method: :delete, data: { confirm: 'Are you sure?' } %></td>
+  </tr>
+<% end %>
+</table>
+
+<br />
+
+<%= link_to 'New Service Credential', new_service_credential_path %>

data/app/views/taverna_player/service_credentials/new.html.erb

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+<%
+  # Copyright (c) 2013 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>New service_credential</h1>
+
+<%= render 'form', :service_credential => @service_credential %>
+
+<%= link_to 'Back', service_credentials_path %>

data/app/views/taverna_player/service_credentials/show.html.erb

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+<%
+  # Copyright (c) 2013 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>Service Credential</h1>
+
+<p>
+  <b>Name:</b>
+  <%= @service_credential.name %>
+</p>
+
+<p>
+  <b>Description:</b>
+  <%= @service_credential.description %>
+</p>
+
+<p>
+  <b>URI:</b>
+  <%= @service_credential.uri %>
+</p>
+
+<p>
+  <b>Login:</b>
+  <%= @service_credential.login %>
+</p>
+
+<%= link_to 'Edit', edit_service_credential_path(@service_credential) %> |
+<%= link_to 'Back', service_credentials_path %>

data/config/routes.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 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
+#------------------------------------------------------------------------------
+
+TavernaPlayer::Engine.routes.draw do
+  resources :runs, :except => :edit do
+    member do
+      put "cancel", :action => "cancel"
+      get "input/:port", :action => "input"
+      get "output/:port(/*path)", :action => "output"
+
+      scope "download" do
+        get "log", :action => "download_log"
+        get "results", :action => "download_results"
+        get "output/:port", :action => "download_output"
+      end
+
+      scope "interaction" do
+        get ":int_id", :action => "read_interaction"
+        post ":int_id", :action => "write_interaction"
+      end
+    end
+  end
+
+  resources :service_credentials
+end

data/db/migrate/20130313105546_create_taverna_player_runs.rb

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+class CreateTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    create_table :taverna_player_runs do |t|
+      t.string :run_id
+      t.string :state, :default => "pending", :null => false
+      t.datetime :create_time
+      t.datetime :start_time
+      t.datetime :finish_time
+      t.integer :workflow_id, :null => false
+
+      t.timestamps
+    end
+
+    add_index :taverna_player_runs, :run_id
+  end
+end

data/db/migrate/20130315163019_create_taverna_player_run_ports.rb

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+class CreateTavernaPlayerRunPorts < ActiveRecord::Migration
+  def change
+    create_table :taverna_player_run_ports do |t|
+      t.string :name
+      t.string :value
+      t.string :file
+      t.string :port_type
+      t.references :run
+
+      t.timestamps
+    end
+
+    add_index :taverna_player_run_ports, :run_id
+  end
+end

data/db/migrate/20130318170744_add_attachment_file_to_taverna_player_run_ports.rb

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+class AddAttachmentFileToTavernaPlayerRunPorts < ActiveRecord::Migration
+  def change
+    remove_column :taverna_player_run_ports, :file
+    add_attachment :taverna_player_run_ports, :file
+  end
+end

data/db/migrate/20130319183634_create_delayed_jobs.rb

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+class CreateDelayedJobs < ActiveRecord::Migration
+  def self.up
+    create_table :delayed_jobs, :force => true do |table|
+      table.integer  :priority, :default => 0      # Allows some jobs to jump to the front of the queue
+      table.integer  :attempts, :default => 0      # Provides for retries, but still fail eventually.
+      table.text     :handler                      # YAML-encoded string of the object that will do work
+      table.text     :last_error                   # reason for last failure (See Note below)
+      table.datetime :run_at                       # When to run. Could be Time.zone.now for immediately, or sometime in the future.
+      table.datetime :locked_at                    # Set when a client is working on this object
+      table.datetime :failed_at                    # Set when all retries have failed (actually, by default, the record is deleted instead)
+      table.string   :locked_by                    # Who is working on this object (if locked)
+      table.string   :queue                        # The name of the queue this job is in
+      table.timestamps
+    end
+
+    add_index :delayed_jobs, [:priority, :run_at], :name => 'delayed_jobs_priority'
+  end
+
+  def self.down
+    drop_table :delayed_jobs
+  end
+end

data/db/migrate/20130320102600_add_status_message_to_taverna_player_runs.rb

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+class AddStatusMessageToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :status_message, :string
+  end
+end

data/db/migrate/20130321100110_add_depth_and_metadata_to_taverna_player_run_ports.rb

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+class AddDepthAndMetadataToTavernaPlayerRunPorts < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_run_ports, :depth, :integer, :default => 0
+    add_column :taverna_player_run_ports, :metadata, :text
+  end
+end

data/db/migrate/20130704095504_add_attachment_results_to_taverna_player_runs.rb

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+class AddAttachmentResultsToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_attachment :taverna_player_runs, :results
+  end
+end

data/db/migrate/20130705142704_add_embedded_to_taverna_player_runs.rb

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+class AddEmbeddedToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :embedded, :boolean, :default => false
+  end
+end