taverna-player 0.1.0

data/app/models/taverna_player/interaction.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
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  class Interaction < ActiveRecord::Base
+    attr_accessible :displayed, :feed_reply, :page, :replied, :unique_id
+
+    belongs_to :run, :class_name => "TavernaPlayer::Run"
+
+    validates_presence_of :unique_id
+    validates_uniqueness_of :unique_id
+    validates_presence_of :serial
+    validates_uniqueness_of :serial, :scope => :run_id,
+      :message => "Interaction serial number should be unique for a run"
+  end
+end

data/app/models/taverna_player/run.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
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+
+  # This class represents a workflow run. It may be yet to run, running or
+  # finished. All inputs and outputs can be accessed via this class.
+  class Run < ActiveRecord::Base
+    include TavernaPlayer::Concerns::Models::Run
+
+    ##
+    # :method: create_time
+    # :call-seq:
+    #   create_time -> datetime
+    #
+    # The time this run was created on the Taverna Server.
+
+    ##
+    # :method: cancelled?
+    # :call-seq:
+    #   cancelled? -> boolean
+    #
+    # Has this run been cancelled?
+
+    ##
+    # :method: complete?
+    # :call-seq:
+    #   complete? -> boolean
+    #
+    # Is this run complete? If a run is finished or cancelled or failed then
+    # it is complete.
+
+    ##
+    # :method: embedded?
+    # :call-seq:
+    #   embedded? -> boolean
+    #
+    # Is this run an embedded run? This helps determine if a run should be
+    # treated differently, e.g. in the views, if it is running embedded within
+    # another location or website.
+
+    ##
+    # :method: failed?
+    # :call-seq:
+    #   failed? -> boolean
+    #
+    # Did this run finish abnormally or with an error?
+
+    ##
+    # :method: finish_time
+    # :call-seq:
+    #   finish_time -> datetime
+    #
+    # The time this run finished running on Taverna Server.
+
+    ##
+    # :method: finished?
+    # :call-seq:
+    #   finished? -> boolean
+    #
+    # Has this run finished normally?
+
+    ##
+    # :method: has_parent?
+    # :call-seq:
+    #   has_parent? -> boolean
+    #
+    # A run will have a parent if it is a child run as part of a sweep.
+
+    ##
+    # :method: name
+    # :call-seq:
+    #   name -> string
+    #
+    # The name (mnemonic) of this run.
+
+    ##
+    # :method: root_ancestor
+    # :call-seq:
+    #   root_ancestor -> run
+    #
+    # Gets the ultimate ancestor of this run, which may not be its immediate
+    # parent.
+
+    ##
+    # :method: running?
+    # :call-seq:
+    #   running? -> boolean
+    #
+    # Is this run still running on Taverna Server?
+
+    ##
+    # :method: start_time
+    # :call-seq:
+    #   start_time -> datetime
+    #
+    # The time this run started running on the Taverna Server.
+
+    ##
+    # :method: state
+    # :call-seq:
+    #   state -> symbol
+    #
+    # The state of this run. Possible states are :pending, :initialized,
+    # :running, :finished, :cancelled or :failed.
+
+  end
+end

data/app/models/taverna_player/run_port.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
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+
+  # This class is the superclass of the input and output port types
+  # RunPort::Input and RunPort::Output, respectively. It holds much common
+  # functionality.
+  #
+  # A port can hold either a text value or a file.
+  class RunPort < ActiveRecord::Base
+
+    MAXIMUM_DATABASE_VALUE_SIZE = 255  # :nodoc:
+
+    self.inheritance_column = "port_type"
+
+    belongs_to :run, :class_name => "TavernaPlayer::Run"
+
+    validates_presence_of :name
+    validates_uniqueness_of :name, :scope => [:run_id, :port_type]
+
+    attr_accessible :depth, :file, :name, :value
+
+    has_attached_file :file,
+      :path => File.join(TavernaPlayer.file_store, ":class/:attachment/:id/:filename"),
+      :url => :file_url_via_run,
+      :default_url => ""
+
+    default_scope order("lower(name) ASC")
+
+    # If there is both a value and a file, then prefer the file. If the file
+    # is changed, delete the value. This must be run before "process_value"!
+    before_save :delete_value, :if => :file_file_name_changed?
+
+    # Overflow the value into a file if it is too big. Don't try to process
+    # the value if the file has changed. This must run after "delete_value"!
+    before_save :process_value, :if => :value_changed?, :unless => :file_file_name_changed?
+
+    # :call-seq:
+    #   display_name -> string
+    #
+    # Convert this port's name to a more presentable form. In practice this
+    # means converting underscores (_) to spaces, while preserving case.
+    def display_name
+      name.gsub('_', ' ')
+    end
+
+    # :call-seq:
+    #   value_preview -> string
+    #
+    # Show up to the first 256 characters of the port's value. This returns
+    # nil if the port has a file instead of a value.
+    def value_preview
+      self[:value]
+    end
+
+    # :call-seq:
+    #   value -> string
+    #
+    # Return the value held in this port if there is one.
+    def value
+      v = self[:value]
+      if !v.blank? && !file.path.blank?
+        File.read(file.path)
+      else
+        v
+      end
+    end
+
+    private
+
+    def delete_value
+      self[:value] = nil
+    end
+
+    # If the value is too big to fit in the database then overflow it into a
+    # file.
+    def process_value
+      v = self[:value]
+
+      if !v.blank? && v.size > MAXIMUM_DATABASE_VALUE_SIZE
+        self[:value] = v[0...MAXIMUM_DATABASE_VALUE_SIZE]
+        save_value_to_file(v)
+      else
+        self.file = nil unless file.path.blank?
+      end
+    end
+
+    def save_value_to_file(v)
+      Dir.mktmpdir("#{id}", Rails.root.join("tmp")) do |tmp_dir|
+        tmp_file_name = File.join(tmp_dir, "#{name}.txt")
+
+        File.write(tmp_file_name, v.force_encoding("UTF-8"))
+
+        self.file = File.new(tmp_file_name)
+      end
+    end
+  end
+
+  # This class represents a workflow input port.
+  class RunPort::Input < RunPort
+
+    private
+
+    def file_url_via_run
+      "/runs/#{run_id}/input/#{name}"
+    end
+  end
+
+  # This class represents a workflow output port.
+  class RunPort::Output < RunPort
+
+    attr_accessible :metadata
+
+    serialize :metadata
+
+    private
+
+    def file_url_via_run
+      "/runs/#{run_id}/output/#{name}"
+    end
+
+    public
+
+    ##
+    # :method: metadata
+    # :call-seq:
+    #   metadata -> hash
+    #
+    # Get the size and type metadata for this output port in a Hash. For a
+    # list output it might look like this:
+    #
+    #  {
+    #    :size => [12, 36509],
+    #    :type => ["text/plain", "image/png"]
+    #  }
+
+  end
+end

data/app/models/taverna_player/service_credential.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
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+
+  # This class represents a credential for authentication to a service during
+  # a workflow run.
+  class ServiceCredential < ActiveRecord::Base
+    attr_accessible :description, :login, :name, :password,
+      :password_confirmation, :uri
+
+    validates :uri, :presence => true
+    validates :login, :presence => true
+    validates :password, :presence => true
+    validates :password_confirmation, :presence => true
+    validates :password, :confirmation => true
+
+    ##
+    # :method: description
+    # :call-seq:
+    #   description -> string
+    #
+    # The description of the service or credential.
+
+    ##
+    # :method: login
+    # :call-seq:
+    #   login -> string
+    #
+    # The login name (or user name) used to log in to the service.
+
+    ##
+    # :method: name
+    # :call-seq:
+    #   name -> string
+    #
+    # The name of the service.
+
+    ##
+    # :method: uri
+    # :call-seq:
+    #   uri -> string
+    #
+    # The URI of the service, returned as a string.
+
+  end
+end

data/app/views/layouts/taverna_player/embedded.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
+%>
+
+<!DOCTYPE html>
+
+<html>
+  <head>
+    <title>Taverna Player</title>
+    <%= stylesheet_link_tag    "application", :media => "all" %>
+    <%= javascript_include_tag "application" %>
+    <%= csrf_meta_tags %>
+  </head>
+  <body>
+
+    <%= yield %>
+
+  </body>
+</html>

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

@@ -0,0 +1,19 @@
+<%
+  # 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
+%>
+
+<div id="run-button">
+  <% if run.complete? %>
+    <%= link_to 'Delete', run, :method => :delete, :data => { confirm: 'Are you sure?' } -%>
+  <% else %>
+    <%= link_to "Cancel", cancel_run_path(run.id), :method => :put, :data => { confirm: "Are you sure?" } -%>
+  <% end %>
+</div>

data/app/views/taverna_player/runs/_info.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
+%>
+
+<div id="run-info">
+  <p>
+    <b>Run:</b>
+    <%= run.run_id %>
+  </p>
+
+  <p>
+    <b>Name:</b>
+    <%= form_for run, :html => {:multipart => true} do |f| %>
+      <%= f.text_field :name %>
+      <%= f.submit "Update" %>
+    <% end %>
+  </p>
+
+  <p>
+    <b>State:</b>
+    <%= run.state %>
+  </p>
+
+  <p>
+    <b>Status message:</b>
+    <%= run.status_message %>
+  </p>
+
+  <p>
+    <b>Create time:</b>
+    <%= run.create_time %>
+  </p>
+
+  <p>
+    <b>Start time:</b>
+    <%= run.start_time %>
+  </p>
+
+  <p>
+    <b>Finish time:</b>
+    <%= run.finish_time %>
+  </p>
+
+  <p>
+    <b>Embedded:</b>
+    <%= run.embedded %>
+  </p>
+</div>