Ok, I don't know if this is the right place to ask about this, but I downloaded
the taverna-t2flow Ruby gem and installed it. When I run the following code:
=====================================================================
require "rubygems"
require "t2flow/model.rb"
require "t2flow/parser.rb"
out_file = File.new("pathways_and_gene_annotations_forqtl_region_290738.dot",
"w+")
workflow =
File.new("pathways_and_gene_annotations_forqtl_region_290738.t2flow", "r").read
model = T2Flow::Parser.new.parse(workflow)
T2Flow::Dot.new.write_dot(out_file, model)
=====================================================================
I get the error:
uninitialized constant T2Flow::Dot (NameError)
I did a T2Flow.constants and got the following result:
["DataflowAnnotation", "ProcessorLinks", "Source", "Parser", "Model",
"Dataflow", "Coordination", "Processor", "Sink", "Datalink"]
As you can see, there is not Dot class in there. What do I do?
--Kamran
On 27 Mar 2012, at 17:04, Kamran Soomro wrote:
> Hi Rob,
>
> Thanks a lot for the link. I absolutely do not mind Ruby if I just have to
> use the script as a black box. The less work for me, the better :) A
> question: why would the plugins need to be loaded for the conversion process?
> If it's just for the colour conversions, I am not interested in those as I
> actually need to process the graphs further programmatically. I don't care
> how they look. Is there no way I can circumvent the need for loading the
> plugins?
>
> --Kamran
>
> P.S., I forgot to link to the tutorial in the previous email. My bad.
> http://www.mygrid.org.uk/usermanual1.6/executeworkflowprogram.html
>
> On 27 Mar 2012, at 16:50, Robert Haines wrote:
>
>> Hi Kamran,
>>
>>> Thanks a lot for the quick reply. Assuming that I have all the
>>> plugins available, do I have to perform any other initialisations to
>>> get these methods to work or simply constructing the appropriate
>>> objects would be enough? Using a bit of Google-Fu, I found the
>>> following tutorial. However, it is for Taverna 1.6. Do I have to
>>> perform any of the steps mentioned in it? If not, any documentation
>>> that would help me get started quickly?
>>
>> Something else that you could try, if you don't mind a bit of ruby, is
>> the taverna-t2flow gem: https://rubygems.org/gems/taverna-t2flow
>>
>> It can parse t2flow and produce the necessary data file needed by dot to
>> produce the workflow image. I believe that this is what myExperiment.org
>> uses to create its images.
>>
>> Note that, as David mentioned earlier, this code will not know about all
>> the different activities that could be present as plugins but you
>> probably wouldn't find it too difficult to add colour conversions to
>> that code should you need them. You might not even need to go that far
>> if the workflows you are using don't use any extra plugins.
>>
>> Best wishes,
>> Rob
>>
>>> On 27 Mar 2012, at 16:27, David Withers wrote:
>>>
>>>> Hi Kamran,
>>>>
>>>> To generate the DOT programmatically you will have to :
>>>>
>>>> 1. Parse the workflow file to create a Dataflow object - see
>>>> net.sf.taverna.t2.workbench.file.impl.T2DataflowOpener.openDataflow()
>>>>
>>>>
>> 2. Generate a Graph from the Dataflow -
>> net.sf.taverna.t2.workbench.models.graph.GraphController.generateGraph()
>>>> 3. Generate the DOT from the Graph -
>>>> net.sf.taverna.t2.workbench.models.graph.DotWriter.writeGraph()
>>>>
>>>> It's not quite as simple as this though; as Taverna has a plugin
>>>> based architecture you will have to ensure that you also have all
>>>> the required activity plugins for all the activity types that your
>>>> workflows use.
>>>>
>>>> David.
>>>>
>>>> On 27 Mar 2012, at 14:32, Kamran Soomro wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am looking to convert a bunch of Taverna 2 workflows to the DOT
>>>>> language in bulk as I don't want to load up each workflow in the
>>>>> application and save it manually. I was wondering if there was
>>>>> any way to do that? I have looked at the command line tool but
>>>>> apparently it doesn't support exporting the workflows to DOT. I
>>>>> see that there is an API method to write a Taverna graph to a DOT
>>>>> file. If there is no existing way to do what I want, I am ready
>>>>> to write my own code and convert the workflow through the API. In
>>>>> that case, I would appreciate it somebody can point me to any
>>>>> tutorials which can help to understand how I can load the
>>>>> workflows and convert them programmatically. Thank you.
>>>>>
>>>>> --Kamran
>>>>>
>>>>
>>>> -- David Withers School of Computer Science, University of
>>>> Manchester, Oxford Road, Manchester, M13 9PL, UK. +44 (0)161 275
>>>> 0683
>>>>
>>>>
>>>>
>>>>
>>>>
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>>
>> --
>> Robert Haines
>> myGrid Team
>> School of Computer Science
>> University of Manchester
>>
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