Nothing
capture.essentia <- function(scriptcall = "", linenumber = "all", separator = " ")
{
argumentlist <- read.delim(header=FALSE,sep=separator,quote="\"'",comment.char="#",text=scriptcall)[1,]
print(argumentlist)
tmpcommand1 <- FALSE
ignoreargs <- FALSE
if (length(argumentlist)==1) {
argumentlist <- matrix(argumentlist,1,2)
argumentlist[,2] <- "ignore"
ignoreargs <- TRUE
}
file <- sprintf("%s",argumentlist[1,1])
print(file)
commandcount <- 1
lineold <- ""
if (linenumber == "all") {
lines <- readLines(file)
}
else {
lines <- readLines(file)[linenumber]
}
for (line in lines) {
if (line != "") {
if (grepl(".R", file)) {
line <- substr(line, 2, nchar(line))
if (line == "THIS IS THE END OF MY ESSENTIA COMMANDS") {
break
}
}
line <- paste(lineold, line, sep = "")
if (substr(line, nchar(line), nchar(line)) == "\\") {
lineold <- substr(line, 1, nchar(line) - 1)
next
}
else {
lineold <- ""
}
if ((length(argumentlist) > 1) && (ignoreargs == FALSE)) {
for (index in seq(2,length(argumentlist))) {
bashsub_type <- 0
while (bashsub_type < 2) {
if (bashsub_type == 0) {
line <- strsplit(line,sprintf("\\$%i",index - 1))[[1]]
}
else {
line <- strsplit(line,sprintf("\\$\\{%i\\}",index - 1))[[1]]
}
if (length(line) > 1) {
for (i in seq(1,length(line)-1)) {
print(line[i])
print(argumentlist[1,index])
line[i] <- paste0(line[i],sprintf("%s",argumentlist[1,index]))
}
}
line <- paste(line,collapse="")
bashsub_type <- bashsub_type + 1
}
}
}
print(line)
if (((substr(line, 1, 8) == "ess exec") && (!grepl("#Rignore",
line))) || ((substr(line, 1, 10) == "ess stream" ||
substr(line, 1, 9) == "ess query") && (grepl("#Rinclude",
line)))) {
quotes <- grepRaw("\"", line, all = TRUE)
aq <- quotes[[length(quotes)]]
if ((substr(line, 1, 10) == "ess stream") || (substr(line,
1, 8) == "ess exec")) {
line <- paste(substr(line, 1, aq - 1), "; echo 'RSTOPHERE'",
substr(line, aq, nchar(line)), sep = "")
}
else {
line <- paste(substr(line, 1, aq), "; echo 'RSTOPHERE'",
substr(line, aq + 1, nchar(line)), 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)
}
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) {
if (varname == "command") {
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
numrows <- length(get(sprintf("%s%i", varname, commandcount))[,1])
print(get(sprintf("%s%i", varname, commandcount))[1:min(10,numrows),])
print(sprintf("---------------- There are a total of %i Rows ----------------", numrows))
commandcount <- commandcount + 1
}
else {
assign(sprintf("%s%i", varname, file), t2[index:(which(t2[,
1] == "RSTOPHERE")[[file]] - 1), 1:ncol(t2)],
inherits = TRUE)
index <- which(t2[, 1] == "RSTOPHERE")[[file]] +
1
numrows <- length(get(sprintf("%s%i", varname, file))[,1])
print(get(sprintf("%s%i", varname, file))[1:min(10,numrows),])
print(sprintf("---------------- There are a total of %i Rows ----------------", numrows))
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")))) {
if (varname == "command") {
if (commandcount == 1) {
tmpcommand1 <- t3
numrows <- length(tmpcommand1[,1])
print(tmpcommand1[1:min(10,numrows),])
print(sprintf("---------------- There are a total of %i Rows ----------------", numrows))
}
else {
assign(sprintf("command%i", commandcount),
t3, inherits = TRUE)
numrows <- length(get(sprintf("%s%i", varname, commandcount))[,1])
print(get(sprintf("command%i", commandcount))[1:min(10,numrows),])
print(sprintf("---------------- There are a total of %i Rows ----------------", numrows))
print(sprintf("---------------- Output Stored in command%i ----------------",
commandcount))
}
}
else {
assign(sprintf("%s", varname), t3, inherits = TRUE)
numrows <- length(get(sprintf("%s", varname))[,1])
print(get(sprintf("%s", varname))[1:min(10,numrows),])
print(sprintf("---------------- There are a total of %i Rows ----------------", numrows))
print(sprintf("---------------- Output Stored in %s ----------------",
varname))
}
commandcount <- commandcount + 1
}
}
}
remove(t2)
if ((file > 1) && (separate)) {
if (varname == "command") {
print(sprintf("---------------- Stream Completed: %i files stored in %i commands: command%i to command%i ----------------",
file, file, commandcount - file, 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("command%i", commandcount),
t2[1:file, 1:ncol(t2)], inherits = TRUE)
numrows <- length(get(sprintf("command%i", commandcount))[,1])
print(get(sprintf("command%i", commandcount))[1:min(10,numrows),])
print(sprintf("---------------- There are a total of %i Files ----------------", numrows))
print(sprintf("---------------- Filenames stored in command%i ----------------",
commandcount))
commandcount <- commandcount + 1
close(t1)
remove(t1)
remove(t2)
}
}
else {
print(sprintf("---------------- Stream Completed: %i files stored in %i commands: %s%i to %s%i ----------------",
file, file, varname, 1, varname, file))
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, file + 1),
t2[1:file, 1:ncol(t2)], inherits = TRUE)
numrows <- length(get(sprintf("%s%i", varname, file + 1))[,1])
print(get(sprintf("%s%i", varname, file +
1))[1:min(10,numrows),])
print(sprintf("---------------- There are a total of %i Files ----------------", numrows))
print(sprintf("---------------- Filenames stored in %s%i ----------------",
varname, file + 1))
close(t1)
remove(t1)
remove(t2)
}
}
}
}
else {
if (line != "") {
system(line)
}
}
}
}
if ((commandcount == 2) && (tmpcommand1 != FALSE)) {
return(tmpcommand1)
}
else {
if ((commandcount > 2) && (tmpcommand1 != FALSE)) {
assign("command1",tmpcommand1,inherits=TRUE)
print("---------------- First Command's Output Stored in command1 ----------------")
}
}
print(sprintf("---------------- There are a total of %i commands ----------------",
commandcount - 1))
remove(colspec, commandcount, index, line, lineold, lines,
separate, t3, varname, tmpcommand1)
}
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