Top Level Namespace

Defined Under Namespace

Modules: Paperclip, TavernaPlayer

Instance Method Summary collapse

Instance Method Details

#cannot_inline(port, index = []) ⇒ Object 



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# File 'lib/generators/templates/callbacks/render_callbacks.rb', line 51

def cannot_inline(port, index = [])
  "Sorry but we cannot show this type of content in the browser. Please " +
   link_to("download it", port.path(index)) + " to view it on " +
   "your local machine."
end

#cannot_inline_tp_default(port, index = []) ⇒ Object 



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# File 'lib/taverna_player/render_callbacks.rb', line 34

def cannot_inline_tp_default(port, index = [])
  "Sorry but we cannot show this type of content in the browser. Please " +
   link_to("download it", port.path(index)) + " to view it on " +
   "your local machine."
end

#empty_port(port, _) ⇒ Object

Rendering an empty port has no need of the index parameter.



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# File 'lib/generators/templates/callbacks/render_callbacks.rb', line 58

def empty_port(port, _)
  "<div>&lt;empty port&gt;</div>"
end

#empty_tp_default(port, _) ⇒ Object 



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# File 'lib/taverna_player/render_callbacks.rb', line 40

def empty_tp_default(port, _)
  "<div>&lt;empty port&gt;</div>"
end

#format_text(port, index = []) ⇒ Object

These methods are the default renderer callbacks that Taverna Player uses. If you customize (or add to) the methods in this file you must register them in the Taverna Player initializer. These methods will not override the defaults automatically.

Each method MUST accept two parameters:

* The first (port) is the port to be rendered.
* The second (index) is the index into the port. For singleton ports this
  will be the empty list.

Note that you can use most of the ActiveView Helpers here as global methods but the image_tag() method does not work as explained below.



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# File 'lib/generators/templates/callbacks/render_callbacks.rb', line 26

def format_text(port, index = [])
  # Use CodeRay to format text so that newlines are respected.
  content = CodeRay.scan(port.value(index), :text).div(:css => :class)

  # Use auto_link to turn URI-like text into links.
  auto_link(content, :html => { :target => '_blank' }, :sanitize => false)
end

#format_text_tp_default(port, index = []) ⇒ Object

Copyright © 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



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# File 'lib/taverna_player/render_callbacks.rb', line 13

def format_text_tp_default(port, index = [])
  content = CodeRay.scan(port.value(index), :text).div(:css => :class)
  auto_link(content, :html => { :target => '_blank' }, :sanitize => false)
end

#format_xml(port, index = []) ⇒ Object 



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# File 'lib/generators/templates/callbacks/render_callbacks.rb', line 34

def format_xml(port, index = [])
  # Make sure XML is indented consistently.
  out = String.new
  REXML::Document.new(port.value(index)).write(out, 1)
  CodeRay.scan(out, :xml).div(:css => :class, :line_numbers => :table)
end

#format_xml_tp_default(port, index = []) ⇒ Object 



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# File 'lib/taverna_player/render_callbacks.rb', line 18

def format_xml_tp_default(port, index = [])
  out = String.new
  REXML::Document.new(port.value(index)).write(out, 1)
  CodeRay.scan(out, :xml).div(:css => :class, :line_numbers => :table)
end

#list_port(port, index = [], types = nil) ⇒ Object

Rendering a list port requires recursion. In this implementation an extra parameter (types) is added to drive the recursion; we can’t just keep track of depth because we need to know the length of each sub-list - and types can be used to pass that through for us.



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# File 'lib/generators/templates/callbacks/render_callbacks.rb', line 66

def list_port(port, index = [], types = nil)
  types = port.metadata[:type] if types.nil?

  content = "<ol>"
  i = 0
  types.each do |type|
    if type.is_a?(Array)
      content += "<li><br />" +
      list_port(port, index + [i], type) + "</li>"
    else
      content += "<li>(#{type})<p>" +
        TavernaPlayer.port_renderer.render(port, index + [i]) +
        "</p></li>"
    end
    i += 1
  end

  content += "</ol>"
end

#list_tp_default(port, index = [], types = nil) ⇒ Object 



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# File 'lib/taverna_player/render_callbacks.rb', line 44

def list_tp_default(port, index = [], types = nil)
  types = port.metadata[:type] if types.nil?

  content = "<ol>"
  i = 0
  types.each do |type|
    if type.is_a?(Array)
      content += "<li><br />" +
      list_tp_default(port, index + [i], type) + "</li>"
    else
      content += "<li>(#{type})<p>" +
        TavernaPlayer.port_renderer.render(port, index + [i]) +
        "</p></li>"
    end
    i += 1
  end

  content += "</ol>"
end

#player_post_run_callback(run) ⇒ Object 



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# File 'lib/generators/templates/callbacks/worker_callbacks.rb', line 18

def player_post_run_callback(run)
  w = TavernaPlayer::Workflow.find(run.workflow_id)
  puts "Post-run callback called for run '#{run.name}' of workflow '#{w.id}'"
end

#player_pre_run_callback(run) ⇒ Object

Copyright © 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



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# File 'lib/generators/templates/callbacks/worker_callbacks.rb', line 13

def player_pre_run_callback(run)
  w = TavernaPlayer::Workflow.find(run.workflow_id)
  puts "Pre-run callback called for run '#{run.name}' of workflow '#{w.id}'"
end

#player_run_cancelled_callback(run) ⇒ Object 



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# File 'lib/generators/templates/callbacks/worker_callbacks.rb', line 23

def player_run_cancelled_callback(run)
  w = TavernaPlayer::Workflow.find(run.workflow_id)
  puts "Run-cancelled callback called for run '#{run.name}' of workflow '#{w.id}'"
end

#player_run_failed_callback(run) ⇒ Object 



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# File 'lib/generators/templates/callbacks/worker_callbacks.rb', line 28

def player_run_failed_callback(run)
  w = TavernaPlayer::Workflow.find(run.workflow_id)
  puts "Run-failed callback called for run '#{run.name}' of workflow '#{w.id}'"
end

#show_image(port, index = []) ⇒ Object 



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# File 'lib/generators/templates/callbacks/render_callbacks.rb', line 41

def show_image(port, index = [])
  # Can't use image_tag() here because the image doesn't really exist (it's in
  # a zip file, really) and this confuses the Rails asset pipeline.
  tag("img", :src => port.path(index))
end

#show_image_tp_default(port, index = []) ⇒ Object 



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# File 'lib/taverna_player/render_callbacks.rb', line 24

def show_image_tp_default(port, index = [])
  # Can't use image_tag() here because the image doesn't really exist (it's in
  # a zip file, really) and this confuses the Rails asset pipeline.
  tag("img", :src => port.path(index))
end

#workflow_error(port, index = []) ⇒ Object 



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# File 'lib/generators/templates/callbacks/render_callbacks.rb', line 47

def workflow_error(port, index = [])
  link_to("This output is a workflow error.", port.path(index))
end

#workflow_error_tp_default(port, index = []) ⇒ Object 



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# File 'lib/taverna_player/render_callbacks.rb', line 30

def workflow_error_tp_default(port, index = [])
  link_to("This output is a workflow error.", port.path(index))
end