soaplab-users

[Soaplab-users] quotes

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

Hi,

I try to use double quotes in the ACD file for a list.
I must do something wrong because double quotes don't appear in the 
report file where the command line is written.
But I don't know why.

Here is the code for the list
     list: d [
         standard: "Y"
#        template: '-d "$$"'
         comment: 'method -d "$$"'
         default: "swiss"
         comment: "defaults"
         minimum: 1
         values: "nrcrc:non redundant, swiss:SwissProt, 
swisstrembl:UniProt (SwissProt/TrEMBL), trembl_all:TrEMBL, refseq:RefSeq 
protein, ipi:IPI ENSEMBL, gp:GenPept, shuffled:randomized SwissProt, 
microbial:All microbial proteomes (SP format), nrl3d:non redundant 3D 
structure, UniRef100:UniRef100, UniRef90:UniRef90, UniRef50:UniRef50, 
athpep:A. thaliana (from TIGR), worm:Worm (C. elegans), yeast:Yeast (S. 
cerevisiae)"
         delimiter: ", "
         codedelimiter: ":"
         information: "Peptide database used as target."
     ]

And the command line declared in the ACD:
comment: 'method ... $d ...'


Do you know what could be wrong ?
I have tried with \" but nothing appends

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] quotes

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

> I try to use double quotes in the ACD file for a list.
> I must do something wrong because double quotes don't appear in the 
> report file where the command line is written.

> I have tried with \" but nothing appends

double escaped quotes seem to work, such as \\" 

Mahmut

Re: [Soaplab-users] quotes

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

>> I try to use double quotes in the ACD file for a list.
>> I must do something wrong because double quotes don't appear in the 
>> report file where the command line is written.
> 
>> I have tried with \" but nothing appends
> 
> double escaped quotes seem to work, such as \\" 
> 
> Mahmut

Thanks
It is the thing I have missed

-- 
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] quotes

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

Sebastien Moretti a écrit :
>>> I try to use double quotes in the ACD file for a list.
>>> I must do something wrong because double quotes don't appear in the 
>>> report file where the command line is written.
>>
>>> I have tried with \" but nothing appends
>>
>> double escaped quotes seem to work, such as \\"
>> Mahmut
> 
> Thanks
> It is the thing I have missed

Just another problem now.

Double quotes appear in the report file, around the attribute from the 
list, as it should. But the execution fails.

If I copy/paste the command line from the report file, the program runs 
successfully.

Is the command line in the report file the real one ?
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] quotes

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

Hi Sebastien,

> Double quotes appear in the report file, around the attribute from the 
> list, as it should. But the execution fails.
> 
> If I copy/paste the command line from the report file, the program runs 
> successfully.
> 
> Is the command line in the report file the real one ?

It should be but you can double check it by adding a log line in the run
method of the SowaJob class.

        Thread executeThread = getExecuteThread (pb);
        log.info("program and arguments: "+pb.command());
        executeThread.start();

Regards,
Mahmut