soaplab-users

[Soaplab-users] output files not definable on command line

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

Hi

I use an application which adds an extension to input file for output files.
Output files are not sent to stdout
I can change the output root name or keep the same than the input.


How could I define output files in the ACD file ?

Should I directly send them to _R_/RESULTS/.../results/ directory ?
But how ?

Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] output files not definable on command line

[Mahmut U. <ul...@eb...>]

Hi Sebastien,

> I use an application which adds an extension to input file for output files.
> Output files are not sent to stdout
> I can change the output root name or keep the same than the input.
> 
> 
> How could I define output files in the ACD file ?
> 
> Should I directly send them to _R_/RESULTS/.../results/ directory ?
> But how ?

Can you give an example? I'm finding it difficult to understand your
question.

Regards,
Mahmut

Re: [Soaplab-users] output files not definable on command line

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

> Hi Sebastien,
> 
>> I use an application which adds an extension to input file for output files.
>> Output files are not sent to stdout
>> I can change the output root name or keep the same than the input.
>>
>>
>> How could I define output files in the ACD file ?
>>
>> Should I directly send them to _R_/RESULTS/.../results/ directory ?
>> But how ?
> 
> Can you give an example? I'm finding it difficult to understand your
> question.
> 
> Regards,
> Mahmut

When it runs, the program creates output files in ../_R_/SANDBOX/.../:
i_infile.pdf
i_infile.out
...


I would like to put these files in _R_/RESULTS/.../results/
But I don't control their extensions nor their location.

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] output files not definable on command line

[Martin S. <mar...@gm...>]

> How could I define output files in the ACD file ?


You can't (except the file extension). The output file names are hidden to
you (because it is somehow against the spirit of a distributed application
to deal with files). If your application relies on such file naming schema,
you need to write a wrapper (an example of such wrapper - that I can send to
you - would be for the program 'cap' - or a similar name, I do not remember
now, having it on a different computer).

Martin

-- 
Martin Senger
email: mar...@gm...,m.s...@cg...
skype: martinsenger
Sent from: Pasig Riz Philippines.

Re: [Soaplab-users] output files not definable on command line

[Mahmut U. <ul...@eb...>]

>         How could I define output files in the ACD file ?
>  
> You can't (except the file extension). The output file names are
> hidden to you (because it is somehow against the spirit of a
> distributed application to deal with files). If your application
> relies on such file naming schema, you need to write a wrapper (an
> example of such wrapper - that I can send to you - would be for the
> program 'cap' - or a similar name, I do not remember now, having it on
> a different computer).

I had a similar problem when i was integrating one application to
Soaplab. I used the 'default' attribute of the outfile options to
specify the name of the output file my application was expecting. This
worked well however i also needed to add a new check in the getFileName
method of the IOData class for checking whether the output has a default
file name and it is secure to use. This didn't look like against the
spirit of a distributed application but i wasn't quite sure and thought
discussing with you (haven't had a chance before).

Mahmut

Re: [Soaplab-users] output files not definable on command line

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

>>         How could I define output files in the ACD file ?
>>  
>> You can't (except the file extension). The output file names are
>> hidden to you (because it is somehow against the spirit of a
>> distributed application to deal with files). If your application
>> relies on such file naming schema, you need to write a wrapper (an
>> example of such wrapper - that I can send to you - would be for the
>> program 'cap' - or a similar name, I do not remember now, having it on
>> a different computer).
> 
> I had a similar problem when i was integrating one application to
> Soaplab. I used the 'default' attribute of the outfile options to
> specify the name of the output file my application was expecting. This
> worked well however i also needed to add a new check in the getFileName
> method of the IOData class for checking whether the output has a default
> file name and it is secure to use. This didn't look like against the
> spirit of a distributed application but i wasn't quite sure and thought
> discussing with you (haven't had a chance before).
> 
> Mahmut

I will test this.
Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] output files not definable on command line

[Mahmut U. <ul...@eb...>]

> > I had a similar problem when i was integrating one application to
> > Soaplab. I used the 'default' attribute of the outfile options to
> > specify the name of the output file my application was expecting. This
> > worked well however i also needed to add a new check in the getFileName
> > method of the IOData class for checking whether the output has a default
> > file name and it is secure to use.

> I will test this.

Don't forget to add the following check as the first sentence in the
getFileName method of IOData class.

        if (StringUtils.isNotBlank(paramDef.dflt) && !
        paramDef.dflt.startsWith(File.separator))
                    return paramDef.dflt;

It includes an attempt to prevent use of absolute paths but the current
version will not work on windows platform. It should probably be safer
if the check also fails when the file name starts with a reference to
parent directories "..".

Mahmut