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From Daniele Tartarini <d.tartar...@sheffield.ac.uk>
Subject Fwd: Taverna Server REST api provide input files
Date Fri, 29 Apr 2016 10:25:56 GMT
Hi,

I am using a Taverna server 2.5.4 to run a workflow based on Taverna tools
service.

I can run execution correctly following the REST API here:
http://dev.mygrid.org.uk/wiki/display/tav250/Conceptual+Interface

The workflow I'm using is very simple and takes a single input file.

I noted that when I upload to Taverna server input file using:
POST  to
https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/wd/IN

and then associating the port to the file using:

PUT to
https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/input/input/input_file_text
with data
<t2sr:runInput xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/">
<t2sr:file>IN/myfile.txt</t2sr:file> </t2sr:runInput>

execution is correct but input files are hard copied from the
/tmp/42d06756-b9c4-45ef-b69d-a141c69499be
to the Taverna Tool service working folder 'usecase....dir'

I would like to avoid this copy because I would be dealing to substantial
inputs and on a parameter sweep can affect performance.

In Taverna Workbench this issue is solved in a elegant way using the "Set
File Location" tab in the form input window. Files are not copied but
replaced by symbolic links.

*How can I achieve the same result via Taverna server API or a baclava file
(I noted the Set file location information is not saved inside the
baclava)?*

I tried to use the Taverna server API setting the input as reference as
documented  in:
http://dev.mygrid.org.uk/wiki/display/tav250/Conceptual+Interface section:
"Using a File Already on the Taverna Server Installation"

Using:
PUT
https://myserver.ac.uk:8444/taverna-server/rest/runs/88f79b84-6451-4aed-b151-6b051328d922
/input/input/input_file_text

with data ({'content-type': 'application/xml'}):

<t2sr:runInput xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/">
    <t2sr:reference>

https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/
wd/IN/myfile.txt
    </t2sr:reference>
</t2sr:runInput>


I get the following 403 error: filename may not be absolute

*Any Idea how to solve both issues?*

Many thanks in advance.

Cheers

Daniele


-- 
--
Daniele Tartarini

Post-Doctoral Research Associate
Dept. Mechanical Engineering &
INSIGNEO, institute for *in silico* medicine,
University of Sheffield, Sheffield, UK
linkedIn <http://uk.linkedin.com/in/danieletartarini>




-- 
--
Daniele Tartarini

Post-Doctoral Research Associate
Dept. Mechanical Engineering &
INSIGNEO, institute for *in silico* medicine,
University of Sheffield, Sheffield, UK
linkedIn <http://uk.linkedin.com/in/danieletartarini>

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