I'm afraid the website you mention is not really a REST service, it is
just a web-based form that returns HTML. A RESTful webservice would
accept and produce data formats that are accessible programmatically,
like JSON or XML, typically have predictable URI patterns, and operate
using the HTTP verbs and status codes (rather than say an error
message embedded on a web page somewhere). For the web service in
question you would have to programmatically pretend to be a browser,
generating the form data and parsing the returned HTML yourself. You
would have to manually inspect the HTML on the submission form to see
which field names you need to provide.
Taverna does unfortunately not include any built-in features for such
'web scraping', so you would have to do that bit yourself, and as far
as I can tell from a quick glance with this particular web page, would
require a bit of work. It should all be possible by building your own
Beanshell scripts, but you would in effect be programming and not
building workflows (meaning it could take some time); and would have
to learn how to generate form data and extract the bits you need from
the output HTML. Once you have got that far that you can extract the
links to the individual results, you can use the "REST service" in
Taverna to retrieve these, for instance with a pattern like
{url}/codingsequence.fa
If the web service does actually provide a RESTful interface (often
called "API"), or a WSDL/SOAP interface, then those can generally be
easily integrated with your Taverna workflow. If the tool is available
for local installation, you can also use the "Tool Service" in Taverna
to execute the command line locally on your machine (or by SSH). This
is obviously making your workflow less portable to other
machines/users, as they would also need to install the same tool or
have access to the same SSH server. You also need to now maintain
yourself the installation with the latest code and data.
http://dev.mygrid.org.uk/wiki/display/taverna/Tool+service
My first intuition would be to see if there is a web service that can
do the job. http://www.biocatalogue.org/ has a large registry of
these. My second call would be to contact the authors of the desired
service to ask if they have a REST or SOAP service planned.
On Tue, Sep 4, 2012 at 8:10 PM, Merche Castillo <[email protected]> wrote:
>
> Dear friends,
>
> I am working on a gene prediction workflow and as part of it I would like to
> include a REST service for a external gene prediction webserver, AUGUSTUS.
> I'm not very familiar with this kind of service and I'm not sure whether it
> can actually be done.
> This is the submission url:
>
> http://bioinf.uni-greifswald.de/augustus/submission
>
> Results are returned this way:
> http://bioinf.uni-greifswald.de/augustus/cabinet?folder=AUG-1048179296 ,
> where AUG-1048179296 is the job id.
>
> Five different outputs are provided: amino acid sequence, coding sequence,
> gff file, input sequence and an input link to the gbrowser. It would be great
> if I could send my sequence with the REST service and configure a tool to
> retrieve the output files from the returned link.
>
>
>
>
>
>
> Has anyone tried to do something similar?
>
>
> Otherwise I guess I will have no choice but to download the software and call
> it locally.
>
> Regards,
> Merche
>
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--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
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