Nothing
essQuery <- function(essentia, aq = "", flags = "")
{
if (paste0(essentia,aq,flags) != "") {
commandcount <- 1
if (substr(essentia, 1, 3) != "ess") {
flags <- aq
aq <- essentia
essentia <- "ess exec"
}
if (((substr(essentia, 1, 8) == "ess exec") && (!grepl("#Rignore",
flags))) || ((substr(essentia, 1, 10) == "ess stream" ||
substr(essentia, 1, 9) == "ess query") && (grepl("#Rinclude",
flags)))) {
if ((substr(essentia, 1, 10) == "ess stream") || (substr(essentia,
1, 8) == "ess exec")) {
aq <- paste(aq, "; echo 'RSTOPHERE'", sep = "")
}
else {
flags <- paste("; echo 'RSTOPHERE'", flags, sep = " ")
}
line <- paste(essentia, "\"", aq, "\"", flags, sep = " ")
colspec <- TRUE
if (grepl("-notitle", line)) {
colspec <- FALSE
}
varname <- "command"
if (grepl("#R#", line)) {
titleindex <- grepRaw("#R#", line, all = TRUE)
varname <- substr(line, titleindex[[1]] + 3, titleindex[[2]] -
1)
remove(titleindex)
}
pipedline <- pipe(line, open = "r")
t2 <- read.csv(pipedline, header = colspec, sep = ",",
quote = "\"'", comment.char = "#", blank.lines.skip = FALSE,
allowEscapes = TRUE, skip = 0)
close(pipedline)
index <- 1
t3 <- NULL
separate <- grepl(" #Rseparate", line)
for (file in seq(1, length(which(t2[, 1] == "RSTOPHERE")),
1)) {
if (separate) {
assign(sprintf("%s%i", varname, commandcount),
t2[index:(which(t2[, 1] == "RSTOPHERE")[[file]] -
1), 1:ncol(t2)], inherits = TRUE)
index <- which(t2[, 1] == "RSTOPHERE")[[file]] +
1
print(get(sprintf("%s%i", varname, commandcount)))
commandcount <- commandcount + 1
}
else {
t3 <- rbind(t3, t2[index:(which(t2[, 1] == "RSTOPHERE")[[file]] -
1), 1:ncol(t2)])
index <- which(t2[, 1] == "RSTOPHERE")[[file]] +
1
if ((file == length(which(t2[, 1] == "RSTOPHERE")))) {
commandcount <- commandcount + 1
remove(t2)
return(t3)
}
}
}
remove(t2)
if ((file > 1) && (separate)) {
print(sprintf("---------------- Stream Completed: %i files stored in %i commands: %s%i to %s%i ----------------",
file, file, varname, commandcount - file, varname,
commandcount - 1))
if (grepl("#filelist", line)) {
linepart1 <- unlist(strsplit(line, split = " "))
t1 <- pipe(paste(linepart1[[1]], linepart1[[2]],
linepart1[[3]], linepart1[[4]], linepart1[[5]],
linepart1[[6]], "\"aq_pp -f,eok - -d %cols 2> /dev/null | echo %file \"",
sep = " "), open = "r")
t2 <- read.csv(t1, header = FALSE, sep = ",",
quote = "\"'", comment.char = "#", blank.lines.skip = FALSE,
allowEscapes = TRUE, skip = 0)
assign(sprintf("%s%i", varname, commandcount),
t2[1:file, 1:ncol(t2)], inherits = TRUE)
print(get(sprintf("%s%i", varname, commandcount)))
print(sprintf("---------------- Filenames stored in %s%i ----------------",
varname, commandcount))
commandcount <- commandcount + 1
close(t1)
remove(t1)
remove(t2)
}
}
remove(colspec, varname, index, separate, t3)
}
else {
if (((substr(essentia, 1, 8) == "ess exec") && (grepl("#Rignore",
flags))) || ((substr(essentia, 1, 10) == "ess stream" ||
substr(essentia, 1, 9) == "ess query") && (!grepl("#Rinclude",
flags)))) {
line <- paste(essentia, "\"", aq, "\"", flags, sep = " ")
system(line)
}
else {
line <- paste(essentia, aq, flags, sep = " ")
system(line)
}
}
remove(commandcount, line, essentia, aq, flags)
}
}
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