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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: Fwd: Taverna Server REST api provide input files
Date Mon, 02 May 2016 17:37:28 GMT
This was also discussed on dev@taverna - we found it was a bug in the
executeworkflow command line.

> Tracked as https <https://issues.apache.org/jira/browse/TAVERNA-964>://
<https://issues.apache.org/jira/browse/TAVERNA-964>issues.apache.org
<https://issues.apache.org/jira/browse/TAVERNA-964>/
<https://issues.apache.org/jira/browse/TAVERNA-964>jira
<https://issues.apache.org/jira/browse/TAVERNA-964>/browse/TAVERNA-964
<https://issues.apache.org/jira/browse/TAVERNA-964>

It should not be too complicated to fix - perhaps you want to have a go on
a pull request? :-)
On 29 Apr 2016 11:26 a.m., "Daniele Tartarini" <d.tartarini@sheffield.ac.uk>
wrote:

> 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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