Re: [Soaplab-users] Problem with Infile Path

[Sebastien M. <Seb...@un...>]

>     I have (now) a problem with an old application which doesn't seem to
>     accept path provided by SoapLab2 for input file:
>     -in=/opt/tomcat/temp/_R_/SANDBOX/[protein_2d_structure.tmpred]3bd3a626.118f08a1fec.-7ffe/i_infile
> 
> 
> I have tried myself, and I cannot reproduce the error here.
> 
> Could you checks if the path mentioned in your example is a path of the 
> SANDBOX of your current Soaplab2? Because Soaplab2 refuses to take local 
> (local on the server side) files unless they are in its SANDBOX 
> directory. What is the full error message you are getting (something 
> like "Refusing to resolve the reference...")?

The file is exactly where mentioned by the path. It is readable and has 
the proper syntax.

It's my application which cannot read the file with this path.
It doesn't read it in command line, except if I use a path without 
special characters ( [ ] - ), or if I change path to 
/opt/tomcat/temp/_R_/SANDBOX/[protein_2d_structure.tmpred]3bd3a626.118f08a1fec.-7ffe/
and run -in=./i_infile


So, I am looking for a way to protect the path, or to avoid special 
characters inside it.
Something like 	template: "-in=\"$$\""
or		template: "-in='$$'"
but it failed.

> Could you try to run a testing service (which comes with Soaplab2) - 
> using as an input an existing file in your SANDBOX (the example below is 
> just from my machine):
> 
> build/run/run-cmdline-client -protocol local -name testing.files -w -r 
> input_url 
> /home/senger/soaplab2/_R_/SANDBOX/\[classic.helloworld\]-24c8efb0.117ea7cd13f.-8000/o_output

Other services, like EMBOSS services with infile, work fine.

> This calls works fine on my machine, how about on yours?
> 
> Thanks,
> Martin

-- 
Sébastien Moretti
SIB, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221