Taverna 2 Interaction Gem
- Author
-
Emmanuel Tagarira
- Version
-
0.0.0
- Contact
- URL
- Licence
-
LGPL 3 (See LICENCE or www.gnu.org/licenses/lgpl.html)
- Copyright
-
© 2008-2009 University of Manchester, UK
Synopsis
This is a Ruby library to support the interaction with Taverna version 2 workflows (T2Flows). This relies on the functionality provided by the libxml library. To be able to utilise this gem to its full potential, you will need to have the following installed on your system.
-
GraphViz (a graph visualization package)
-
Rdoc gem
-
Darkfish-Rdoc gem
The T2Flow Model Implementation
Much like the Taverna 1 Scufl model, T2Flows contain Processors, Sinks, and Sources. T2Flows however, encapsulate these elements within Dataflow objects. A Dataflow objects is the container for all the different elements present within the Taverna 2 workflows, hence a single T2Flow may have one or more dataflows. WorkflowDescriptions and Links, from the original Taverna 1 workflows (Scufl), have been renamed in T2Flows to DataflowAnnotations and Datalinks respectively. DataflowAnnotations, however, allow for multiple titles, authors, and descriptions, as opposed to the single value attributes held for Scufls.
Installation
To install the gems required by the Taverna 2 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-t2flow
Usage
To be able to generate at least a T2Flow model using the gem, you need to include in your ruby code the following lines:
require "t2flow/model.rb"
require "t2flow/parser.rb"
To generate the model you can then use the gem as follows:
foo = File.new("path/to/workflow/file", "r")
= T2Flow::Parser.new.parse(foo)
Alternatively:
foo = File.new("path/to/workflow/file", "r").read
= T2Flow::Parser.new.parse(foo)
You will then be able to use your T2Flow 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
= T2Flow::Parser.new.parse(foo)
To be enable you to draw images of the T2Flow, you need to include:
require "t2flow/dot.rb"
To be able to use any functionality included in “t2flow/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 T2Flow as follows.
out_file = File.new("path/to/file/you/want/the/dot/script/to/be/written", "w+")
T2Flow::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