Nothing
library("qaqc")
##First read in the arguments listed at the command line
args=(commandArgs(TRUE))
##args is now a list of character vectors
## First check to see if arguments are passed.
## Then cycle through each element of the list and evaluate the expressions.
if(length(args)==0){
stop("No arguments supplied.Please provide '--args study=[studyID] date2process=[DD-MM-YYYY] production=[TRUE|FALSE]'")
##supply default values
}else{
for(i in 1:length(args)){
eval(parse(text=args[[i]]))
}
print(study)
today = date2process
#make date2process a date object
print(today)
## today = "2010-03-22"
toddot <- sub("-", ".", today) #replace first '-'
toddot <- sub("-", ".", toddot)#replace second '-'
## toddot = "22.03.2010"
if (production){
print("Running on Production")
server.share <- file.path("", "", "hlwsfshr10", "sa200400214")#is this used? how is it passed to qaqc
gsk.com <- "bjw34032@gsk.com,cf984373@gsk.com"
mail.text <- paste(today, ", ", sep="")
data <- file.path("", "cic_data", "Oncology", study)
dicom <- file.path("", "scratch", study, "dicom")
nifti <- file.path(data, "nifti")
scripts <- file.path(data, "scripts")
log <- file.path(data, "logs")
logfile <- file.path(log, paste(today, ".log", sep=""))
domfile <- file.path(log, paste(today, "_domain.txt", sep=""))
source(file.path(data, "scripts", paste(tolower(study), "qaqc.R", sep="_")))
}
else{ print("Running on Development")
server.share <- file.path("", "", "hlwsfshr10", "sa200400214")#is this used? how is it passed to qaqc
gsk.com <- "bjw34032@gsk.com,cf984373@gsk.com"
mail.text <- paste(today, ", ", sep="")
data <- file.path("", "cic_data", "Oncology", study, "test")
dicom <- file.path("", "scratch", study, "dicom")
nifti <- file.path(data, "nifti")
scripts <- file.path(data, "scripts")
log <- file.path(data, "logs")
logfile <- file.path(log, paste(today, ".log", sep=""))
domfile <- file.path(log, paste(today, "_domain.txt", sep=""))
source(file.path(data, "scripts", paste(tolower(study), "qaqc.R", sep="_")))
}
}
known.values <- file.path(scripts, paste(tolower(study), "specs.csv", sep="_"))
cat("#### SEARCH ####", file=(con <- file(logfile, "w", encoding="UTF-8")),
fill=TRUE)
close(con)
domain <- file.path("", "usr", "cic", "apps", "bin", "domain")
system(paste(domain, "-search -study_id", study, "-folder 'PI' >", domfile))
domfile.names <- c("Date", "Time", "File.Name", "Document.Size",
"Document.ID", "Mime.Type")
domList <- strsplit(grep(toddot, readLines(domfile), value=TRUE), "[ ]+")
domStrings <- unlist(lapply(domList, function(z) z[4]))
subjectID <- parseDomain(domStrings, index=3)
if (length(subjectID) > 0) {
visitID <- parseDomain(domStrings, c("/","_"), c(4,1))
examID <- parseDomain(domStrings, c("/","_"), c(4,3))
#Call to QAQC may need to be changed to reflect new param list
qaqc(subjectID, visitID, examID, study, logfile, domfile, dicom,
nifti, compare=known.values, pixelData=FALSE, email=gsk.com,
css=file.path(scripts, paste(tolower(study), "css", sep=".")),
verbose=TRUE, debug=FALSE)
} else {
cat("##### No data to download from DOMAIN #####",
file=(con <- file(logfile, "a", encoding="UTF-8")), fill=TRUE)
close(con)
}
subject=subjectID
visit=visitID
exam=examID
study=study
logfile=logfile
domfile=domfile
domdir=dicom
niftidir=nifti
compare=known.values
pixelData=FALSE
email=gsk.com
css=file.path(scripts, paste(tolower(study), "css", sep="."))
verbose=TRUE
debug=FALSE
rm(subject, visit, domdir, niftidir, compare, email, css, verbose, debug)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.