Taverna 1 Interaction Gem
- Authors
-
Stian Soiland, David Withers, Emmanuel Tagarira
- Version
-
0.7.1
- Contact
- URL
- Licence
-
LGPL 3 (See LICENCE or www.gnu.org/licenses/lgpl.html)
- Copyright
-
©2006-2008 University of Manchester, UK
Synopsis
This is a Ruby library to support the interaction with Taverna version 1 workflows (Scufls). This relies on the functionality provided by a graph visualization package called GraphViz.
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 mannie-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")
= Scufl::Parser.new.parse(foo)
Alternatively:
foo = File.new("path/to/workflow/file", "r").read
= 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.
.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
= 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 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, )
`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 workflows to the Taverna Remote Execution service. 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.
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 localhost:8080/tavernaservice/v1/ you can try:
SERVICE = “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
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 end
You can also supply inputs as a hash:
inputs = {} inputs = [“MY_GENE”, “HIS_GENE”] inputs = “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.