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###################################################################################################
# #
# readsmj #
# #
# #
# ==> readsmj&num=xx&nl=xx #
# <== code=xx&nl=xx #
# recnum=xx&name="xx"&plong=xx{&libel="xx"} #
# ... a series of nl lines like that ... #
# Returns data from nl consecutive records starting from rank num of file SMJYT including label #
# if not empty. #
# Code != 0 indicates error. #
# #
###################################################################################################
readsmj <- function(socket = autosocket(), num = 2, nl = 10, recnum.add = FALSE, nature.add = TRUE,
plong.add = FALSE, libel.add = FALSE, sname.add = FALSE, all.add = FALSE)
{
#
# Turn all flags to TRUE when requested:
#
if(all.add) sname.add <- libel.add <- plong.add <- nature.add <- recnum.add <- TRUE
#
# Build the request:
#
request <- paste("readsmj&num=", num, "&nl=", nl, sep = "", collapse = "")
#
# Send request:
#
writeLines(request, socket, sep = "\n")
#
# Read answer from server:
#
s <- readLines(socket, n = 1)
rep <- parser.socket(s)
#
# check answer from server:
#
if(rep[1] != "0") stop("Error from server")
#
# read answer from server:
#
n <- as.numeric(rep[2])
ans <- readLines(socket, n = n)
#
# Put answer into a data.frame:
#
name <- character(n) # the only mandatory one
if(recnum.add) recnum <- numeric(n)
if(nature.add) nature <- factor(character(n), levels = c("00","01","02","03","04","05","06","07"))
if(plong.add) plong <- numeric(n)
if(libel.add) libel <- character(n)
if(sname.add) sname <- character(n)
for(i in seq_len(n)){
tmp <- parser.socket(ans[[i]])
name[i] <- substr(tmp[2], 2, nchar(tmp[2]) - 1)
if(name[i] == "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"){
name[i] <- NA
next
}
if(sname.add) sname[i] <- substr(name[i], 3, nchar(name[i]))
if(recnum.add) recnum[i] <- tmp[1]
if(nature.add) nature[i] <- substr(name[i], 1, 2)
if(plong.add) plong[i] <- tmp[3]
if(libel.add){
if(length(tmp) == 4){
libel[i] <- substr(tmp[4], 2, nchar(tmp[4]) - 1)
} else {
libel[i] <- NA
}
}
}
df <- data.frame(list(name = I(name)))
if(sname.add) df$sname <- sname
if(recnum.add) df$recnum <- recnum
if(nature.add){
levels(nature) <- c("status", "molecule", "journal", "year", "type", "organelle", "division", "dbstrucinfo")
df$nature <- nature
}
if(plong.add) df$plong <- plong
if(libel.add) df$libel <- libel
return(df)
}
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