[Swift-devel] trouble resuming

[Michael Andric]

I'm having trouble resuming swift-jobs.  When resuming, it goes through
'Initializing' every single job in the workflow and just finishes without
actually picking up where it left off.  Below is the swift script.  Thanks
Michael


## type declarations:
type file{}
type Rscript;

## Mediator app declaration:
app (external turn) run_query (string med_args, file config, Rscript code,
file Annot){
    Mediator med_args @filename(code) @filename(Annot);
}

## this process sets parameters and calls Mediator:
loop_query(int vert, string user, string db, string host, string
query_outline, Rscript code, file config, string subject, string h, int
beginTS, int endTS, file Annot){
    string outPrefix = @strcat("gest_vs_nogest_vert",vert,h);
    string med_args = @strcat("--user ","andric"," --conf ",
@filename(config)," --db ", db," --host ", host,
        " --vox ", vert," --subject ", subject," --subquery tsTSVAR","
--begin_ts ",beginTS," --end_ts ",endTS,
        " --query ", query_outline," --r_swift_args ",outPrefix," ",vert,"
",h," ",subject, " --outprefix ", "FAH_Q", " --r_script ", at filename(code));
    external turnpt = run_query(med_args, config, code, Annot);
}

## needed parameters to use Mediator:
string user = @arg("user");
string db = "HEL";
string host = "tp-neurodb.ci.uchicago.edu";
file config<single_file_mapper; file="user.config">;

## mapping the R code:
Rscript code<single_file_mapper; file="Rturning/turnchi_ss2.R">;
file Annot<single_file_mapper;
file="Rturning/resampled_coding_CarStory.txt">;

## variables to move across in the foreach loops:
string declarelist[] = ["ss2"];
string hemilist[] = ["rh"];
int vertices[] = [1:155991:1];
#int vertices[] = [0:1:1];

foreach subject in declarelist{
    foreach h in hemilist{
        int beginTS = 0;
        int endTS = 1254;
        string query_outline = @strcat("SELECT SUBQUERY FROM
",subject,"TS_data",h," WHERE subject = '",subject,"' AND vertex=VOX");
        foreach vert in vertices{
            loop_query(vert, user, db, host, query_outline, code, config,
subject, h, beginTS, endTS, Annot);
        }
    }
}
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