myGrid-taverna-scufl

= Taverna[http://taverna.sourceforge.net] 1 Interaction Gem

Authors:: Stian Soiland, David Withers, Emmanuel Tagarira Version:: 0.6.0 Contact:: [e-mail] URL:: http://taverna.sourceforge.net/ Licence:: LGPL 3 (See LICENCE or http://www.gnu.org/licenses/lgpl.html) Copyright:: (c)2006-2008 University of Manchester, UK

== Synopsis

This is a Ruby library to support the interaction with Taverna[http://taverna.sourceforge.net] version 1 workflows (Scufls). This relies on the functionality provided by a graph visualization package called GraphViz[http://www.graphviz.org/Download.php].

== Installation To install the gems required by the Taverna 1 gem library, type into your command prompt: [sudo] gem install libxml-ruby [sudo] gem install rdoc [sudo] gem install darkfish-rdoc

When you have the required gems on your system, you may install this gem using the following commands: gem sources -a http://gems.github.com [sudo] gem install myGrid-taverna-scufl

== Usage

To be able to generate at least a Scufl model using the gem, you can use the code following code: require "scufl/model.rb" require "scufl/parser.rb"

foo = File.new("path/to/workflow/file", "r") bar = Scufl::Parser.new.parse(foo)

Alternatively: foo = File.new("path/to/workflow/file", "r").read bar = Scufl::Parser.new.parse(foo)

You will then be able to use your Scufl model to retrieve information about the workflow by invoking the different methods and attributes. bar.INVOKED ... where INVOKED is the method or attribute required.

You can also interact with remote workflows. require "open-uri"

foo = Uri.parse("xxxx://uri_to_workflow").read bar = Scufl::Parser.new.parse(foo)

To be enable you to draw images of the Scufl, you need to include: require "scufl/dot.rb"

To be able to use any functionality included in "scufl/dot.rb", you need to have GraphViz[http://www.graphviz.org/Download.php] installed on your system. Once this package has been installed, you may use the gem to draw an image showing the structure of the Scufl as follows. out_file = File.new("path/to/file/you/want/the/dot/script/to/be/written", "w+") Scufl::Dot.new.write_dot(out_file, bar) dot -Tpng -o"path/to/the/output/image" #{out_file.path} The last line draws a PNG image using +out_file+. To learn more about dot, try typing into your command prompt: % man dot or % dot -h

== Taverna Remote Execution Service Client

The library also includes support for submitting Taverna[http://taverna.sourceforge.net] workflows to the Taverna Remote Execution service[2]. This requires the Remote Execution service that has already been installed and configured, and with a client username and password already registered by the administrator of the service. We recommend first testing the service using the Remote Execution service from the Taverna workbench[3].

== Usage

Here's the simplest usecase. Given a Taverna workflow in "workflow.xml" (that produces a value at the port "myOutput") and a Taverna Remote Execution service [2] running at http://localhost:8080/tavernaservice/v1/ you can try:

SERVICE = "http://localhost:8080/tavernaservice/v1/"
workflow = IO.read("workflow.xml")
require 'rubygems'
require 'enactor/client'
enactor = Enactor::Client(SERVICE, "johndoe", "s3cret")
results = enactor.execute_sync(workflow)
print results["myOutput"]

Note that the call to execute_sync() will block until the workflow has been executed on the server. If you want to do this asynchronously, try:

workflow_url = enactor.upload_workflow(workflow)
job_url = enactor.submit_job(workflow_url)
sleep 1 while not enactor.finished?(job_url)
if enactor.get_job_status(job_url) == Enactor::Status.COMPLETE
  results = enactor.get_job_outputs(job_url)
  print results["myOutput"]
end

You can also supply inputs as a hash:

inputs = {}
inputs['gene'] = ["MY_GENE", "HIS_GENE"]
inputs['database'] = "kegg"
results = enactor.execute_sync(workflow, inputs)

or

inputs_url = enactor.upload_data(inputs)
job_url = enactor.submitJob(workflow_url, inputsURL)

See the rdoc documentation of Enactor::Client for more information, try:

help Enactor::Client

Included are also lower level modules Baclava for parsing and creating Baclava data documents, and Scufl for extracting basic information about a workflow, such as which input and output ports it defines.

== References

[1] http://taverna.sourceforge.net [2] http://www.mygrid.org.uk/usermanual1.7/remote_execution_server.html [3] http://www.mygrid.org.uk/usermanual1.7/remote_execution.html