[Swift-user] readdata or csv_mapper problem

[Zhengxiong Hou]

Hello,
  When I try to run many dock jobs on the osg grid sites, 
there are problems for using readdata or csv_mapper. Please 
help to solve it. Here is the experiment at localhost:

  The swift code is as follows:
***********************************************************
[houzx at communicado dock]$ cat grid-many-dock6-string.swift
type file;
(file t) dockcompute (string ligandsfile, string targetlist) 
{
  app {
    rundock ligandsfile targetlist stdout=@filename(t);
    }
}

type params {
      string  ligandsfile;
      string  targetlist;
}

#params pset[] <csv_mapper;file="paramslist.txt">;
doall(params pset[])
{
  foreach params,i in pset {
  #string mol2file <single_file_mapper; file=pset
[i].ligandsfile>;
  #string target <single_file_mapper; file=pset
[i].targetlist>;
  file sout <single_file_mapper; file=@strcat
("/home/houzx/dock-run/databases/results/",pset
[i].targetlist,"-",i,"-stdout.txt")>;
  sout =  dockcompute(pset[i].ligandsfile,pset
[i].targetlist);
 }
}

params p[];
p = readdata("paramslist.txt");
doall(p);
***********************************************************  

The content of "paramslist.txt" is as follows:
[houzx at communicado dock]$ cat paramslist.txt
ligandsfile,targetlist
/home/houzx/dock-
run/databases/KEGG_and_Drugs/D00180.mol2,1F9Y
/home/houzx/dock-
run/databases/KEGG_and_Drugs/D00181.mol2,1F9Y
/home/houzx/dock-
run/databases/KEGG_and_Drugs/D00182.mol2,1F9Y


(1) Use this "readdata" code, and the log file is in the 
attachment "grid-many-dock6-string-20080714-readdata.log".

[houzx at communicado dock]$ swift grid-many-dock6-string.swift
Swift v0.4 swift-r1718 cog-r1934

RunID: 20080714-1405-letz6tcb
Progress:
Execution failed:
        File header does not match type. Expected the 
following header items (in no particular order): 
[ligandsfile, targetlist]. Instead, the header was (again, 
in no particular order): [ligandsfile,targetlist]


(2) Use csv_mapper, and the log file is in the attachment
"grid-many-dock6-string-20080714-1417-csv.log"
[houzx at communicado dock]$ swift grid-many-dock6-string.swift
Swift v0.4 swift-r1718 cog-r1934

RunID: 20080714-1417-pmo8hsjf
Progress:
rundock started
rundock started
rundock started
rundock completed
rundock completed
rundock completed
Final status:  Finished:3
*********************************************************** 
[houzx at communicado dock]$ cat grid-many-dock6-string.swift
type file;
(file t) dockcompute (string ligandsfile, string targetlist) 
{
  app {
    rundock ligandsfile targetlist stdout=@filename(t);
    }
}

type params {
      string  ligandsfile;
      string  targetlist;
}

params pset[] <csv_mapper;file="paramslist.txt">;

foreach params,i in pset {
  file sout <single_file_mapper; file=@strcat
("/home/houzx/dock-run/databases/results/",pset
[i].targetlist,"-",i,"-stdout.txt")>;
  sout =  dockcompute(pset[i].ligandsfile,pset
[i].targetlist);
 }
*********************************************************** 

 But, in the "/home/houzx/dock-run/databases/results/", the 
created files are: null-0-stdout.txt, null-1-stdout.txt,null-
2-stdout.txt.
 It means that "pset[i].targetlist" is set to be "null", not 
the data "1F9Y" from paramslist.txt!
 If I use "Swift v0.3", the created files are:true-0-
stdout.txt,true-1-stdout.txt, true-2-stdout.txt.


Thanks!
B.R.
zhengxiong
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