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.ReplaceVariablesInString <- function(string, replace_values, allow_undefined_key_vars = FALSE) {
# This function replaces all the occurrences of a variable in a string by
# their corresponding string stored in the replace_values.
if (length(strsplit(string, "\\$")[[1]]) > 1) {
parts <- strsplit(string, "\\$")[[1]]
output <- ""
i <- 0
for (part in parts) {
if (i %% 2 == 0) {
output <- paste(output, part, sep = "")
} else {
if (part %in% names(replace_values)) {
output <- paste(output, .ReplaceVariablesInString(replace_values[[part]], replace_values, allow_undefined_key_vars), sep = "")
} else if (allow_undefined_key_vars) {
output <- paste0(output, "$", part, "$")
} else {
stop(paste('Error: The variable $', part, '$ was not defined in the configuration file.', sep = ''))
}
}
i <- i + 1
}
output
} else {
string
}
}
.ReplaceGlobExpressions <- function(path_with_globs, actual_path,
replace_values, tags_to_keep,
dataset_name, permissive) {
# The goal of this function is to replace the shell globbing expressions in
# a path pattern (that may contain shell globbing expressions and Load()
# tags) by the corresponding part of the real existing path.
# What is done actually is to replace all the values of the tags in the
# actual path by the corresponding $TAG$
#
# It takes mainly two inputs. The path with expressions and tags, e.g.:
# /data/experiments/*/$EXP_NAME$/$VAR_NAME$/$VAR_NAME$_*$START_DATE$*.nc
# and a complete known path to one of the matching files, e.g.:
# /data/experiments/ecearth/i00k/tos/tos_fc0-1_19901101_199011-199110.nc
# and it returns the path pattern but without shell globbing expressions:
# /data/experiments/ecearth/$EXP_NAME$/$VAR_NAME$/$VAR_NAME$_fc0-1_$START_DATE$_199011-199110.nc
#
# To do that, it needs also as inputs the list of replace values (the
# association of each tag to their value).
#
# All the tags not present in the parameter tags_to_keep will be repalced.
#
# Not all cases can be resolved with the implemented algorithm. In an
# unsolvable case a warning is given and one possible guess is returned.
#
# In some cases it is interesting to replace only the expressions in the
# path to the file, but not the ones in the file name itself. To keep the
# expressions in the file name, the parameter permissive can be set to
# TRUE. To replace all the expressions it can be set to FALSE.
clean <- function(x) {
if (nchar(x) > 0) {
x <- gsub('\\\\', '', x)
x <- gsub('\\^', '', x)
x <- gsub('\\$', '', x)
x <- unname(sapply(strsplit(x, '[',fixed = TRUE)[[1]], function(y) gsub('.*]', '.', y)))
do.call(paste0, as.list(x))
} else {
x
}
}
strReverse <- function(x) sapply(lapply(strsplit(x, NULL), rev), paste, collapse = "")
if (permissive) {
actual_path_chunks <- strsplit(actual_path, '/')[[1]]
actual_path <- paste(actual_path_chunks[-length(actual_path_chunks)], collapse = '/')
file_name <- tail(actual_path_chunks, 1)
if (length(actual_path_chunks) > 1) {
file_name <- paste0('/', file_name)
}
path_with_globs_chunks <- strsplit(path_with_globs, '/')[[1]]
path_with_globs <- paste(path_with_globs_chunks[-length(path_with_globs_chunks)],
collapse = '/')
path_with_globs <- .ReplaceVariablesInString(path_with_globs, replace_values)
file_name_with_globs <- tail(path_with_globs_chunks, 1)
if (length(path_with_globs_chunks) > 1) {
file_name_with_globs <- paste0('/', file_name_with_globs)
}
right_known <- head(strsplit(file_name_with_globs, '*', fixed = TRUE)[[1]], 1)
right_known_no_tags <- .ReplaceVariablesInString(right_known, replace_values)
path_with_globs_rx <- utils::glob2rx(paste0(path_with_globs, right_known_no_tags))
match <- regexpr(gsub('$', '', path_with_globs_rx, fixed = TRUE), paste0(actual_path, file_name))
if (match != 1) {
stop("Incorrect parameters to replace glob expressions. The path with expressions does not match the actual path.")
}
if (attr(match, 'match.length') - nchar(right_known_no_tags) < nchar(actual_path)) {
path_with_globs <- paste0(path_with_globs, right_known_no_tags, '*')
file_name_with_globs <- sub(right_known, '/*', file_name_with_globs)
}
}
path_with_globs_rx <- utils::glob2rx(path_with_globs)
values_to_replace <- c()
tags_to_replace_starts <- c()
tags_to_replace_ends <- c()
give_warning <- FALSE
for (tag in tags_to_keep) {
matches <- gregexpr(paste0('$', tag, '$'), path_with_globs_rx, fixed = TRUE)[[1]]
lengths <- attr(matches, 'match.length')
if (!(length(matches) == 1 && matches[1] == -1)) {
for (i in 1:length(matches)) {
left <- NULL
if (matches[i] > 1) {
left <- .ReplaceVariablesInString(substr(path_with_globs_rx, 1, matches[i] - 1), replace_values)
left_known <- strReverse(head(strsplit(strReverse(left), strReverse('.*'), fixed = TRUE)[[1]], 1))
}
right <- NULL
if ((matches[i] + lengths[i] - 1) < nchar(path_with_globs_rx)) {
right <- .ReplaceVariablesInString(substr(path_with_globs_rx, matches[i] + lengths[i], nchar(path_with_globs_rx)), replace_values)
right_known <- head(strsplit(right, '.*', fixed = TRUE)[[1]], 1)
}
final_match <- NULL
match_limits <- NULL
if (!is.null(left)) {
left_match <- regexpr(paste0(left, replace_values[[tag]], right_known), actual_path)
match_len <- attr(left_match, 'match.length')
left_match_limits <- c(left_match + match_len - 1 - nchar(clean(right_known)) - nchar(replace_values[[tag]]) + 1,
left_match + match_len - 1 - nchar(clean(right_known)))
if (!(left_match < 1)) {
match_limits <- left_match_limits
}
}
right_match <- NULL
if (!is.null(right)) {
right_match <- regexpr(paste0(left_known, replace_values[[tag]], right), actual_path)
match_len <- attr(right_match, 'match.length')
right_match_limits <- c(right_match + nchar(clean(left_known)),
right_match + nchar(clean(left_known)) + nchar(replace_values[[tag]]) - 1)
if (is.null(match_limits) && !(right_match < 1)) {
match_limits <- right_match_limits
}
}
if (!is.null(right_match) && !is.null(left_match)) {
if (!identical(right_match_limits, left_match_limits)) {
give_warning <- TRUE
}
}
if (is.null(match_limits)) {
stop("Too complex path pattern specified for ", dataset_name,
". Specify a simpler path pattern for this dataset.")
}
values_to_replace <- c(values_to_replace, tag)
tags_to_replace_starts <- c(tags_to_replace_starts, match_limits[1])
tags_to_replace_ends <- c(tags_to_replace_ends, match_limits[2])
}
}
}
if (length(tags_to_replace_starts) > 0) {
reorder <- sort(tags_to_replace_starts, index.return = TRUE)
tags_to_replace_starts <- reorder$x
values_to_replace <- values_to_replace[reorder$ix]
tags_to_replace_ends <- tags_to_replace_ends[reorder$ix]
while (length(values_to_replace) > 0) {
actual_path <- paste0(substr(actual_path, 1, head(tags_to_replace_starts, 1) - 1),
'$', head(values_to_replace, 1), '$',
substr(actual_path, head(tags_to_replace_ends, 1) + 1, nchar(actual_path)))
extra_chars <- nchar(head(values_to_replace, 1)) + 2 - (head(tags_to_replace_ends, 1) - head(tags_to_replace_starts, 1) + 1)
values_to_replace <- values_to_replace[-1]
tags_to_replace_starts <- tags_to_replace_starts[-1]
tags_to_replace_ends <- tags_to_replace_ends[-1]
tags_to_replace_starts <- tags_to_replace_starts + extra_chars
tags_to_replace_ends <- tags_to_replace_ends + extra_chars
}
}
if (give_warning) {
.warning(paste0("Too complex path pattern specified for ", dataset_name,
". Double check carefully the '$Files' fetched for this dataset or specify a simpler path pattern."))
}
if (permissive) {
paste0(actual_path, file_name_with_globs)
} else {
actual_path
}
}
.FindTagValue <- function(path_with_globs_and_tag, actual_path, tag) {
tag <- paste0('\\$', tag, '\\$')
path_with_globs_and_tag <- paste0('^', path_with_globs_and_tag, '$')
parts <- strsplit(path_with_globs_and_tag, '*', fixed = TRUE)[[1]]
parts <- as.list(parts[grep(tag, parts)])
longest_couples <- c()
pos_longest_couples <- c()
found_value <- NULL
for (i in 1:length(parts)) {
parts[[i]] <- strsplit(parts[[i]], tag)[[1]]
if (length(parts[[i]]) == 1) {
parts[[i]] <- c(parts[[i]], '')
}
len_parts <- sapply(parts[[i]], nchar)
len_couples <- len_parts[-length(len_parts)] + len_parts[2:length(len_parts)]
pos_longest_couples <- c(pos_longest_couples, which.max(len_couples))
longest_couples <- c(longest_couples, max(len_couples))
}
chosen_part <- which.max(longest_couples)
parts[[chosen_part]] <- parts[[chosen_part]][pos_longest_couples[chosen_part]:(pos_longest_couples[chosen_part] + 1)]
if (nchar(parts[[chosen_part]][1]) >= nchar(parts[[chosen_part]][2])) {
if (nchar(parts[[chosen_part]][1]) > 0) {
matches <- gregexpr(parts[[chosen_part]][1], actual_path)[[1]]
if (length(matches) == 1) {
match_left <- matches
actual_path <- substr(actual_path, match_left + attr(match_left, 'match.length'), nchar(actual_path))
}
}
if (nchar(parts[[chosen_part]][2]) > 0) {
matches <- gregexpr(parts[[chosen_part]][2], actual_path)[[1]]
if (length(matches) == 1) {
match_right <- matches
found_value <- substr(actual_path, 0, match_right - 1)
}
}
} else {
if (nchar(parts[[chosen_part]][2]) > 0) {
matches <- gregexpr(parts[[chosen_part]][2], actual_path)[[1]]
if (length(matches) == 1) {
match_right <- matches
actual_path <- substr(actual_path, 0, match_right - 1)
}
}
if (nchar(parts[[chosen_part]][1]) > 0) {
matches <- gregexpr(parts[[chosen_part]][1], actual_path)[[1]]
if (length(matches) == 1) {
match_left <- matches
found_value <- substr(actual_path, match_left + attr(match_left, 'match.length'), nchar(actual_path))
}
}
}
found_value
}
.message <- function(...) {
# Function to use the 'message' R function with our custom settings
# Default: new line at end of message, indent to 0, exdent to 3,
# collapse to \n*
args <- list(...)
## In case we need to specify message arguments
if (!is.null(args[["appendLF"]])) {
appendLF <- args[["appendLF"]]
} else {
## Default value in message function
appendLF <- TRUE
}
if (!is.null(args[["domain"]])) {
domain <- args[["domain"]]
} else {
## Default value in message function
domain <- NULL
}
args[["appendLF"]] <- NULL
args[["domain"]] <- NULL
## To modify strwrap indent and exdent arguments
if (!is.null(args[["indent"]])) {
indent <- args[["indent"]]
} else {
indent <- 0
}
if (!is.null(args[["exdent"]])) {
exdent <- args[["exdent"]]
} else {
exdent <- 3
}
args[["indent"]] <- NULL
args[["exdent"]] <- NULL
## To modify paste collapse argument
if (!is.null(args[["collapse"]])) {
collapse <- args[["collapse"]]
} else {
collapse <- "\n*"
}
args[["collapse"]] <- NULL
## Message tag
if (!is.null(args[["tag"]])) {
tag <- args[["tag"]]
} else {
tag <- "* "
}
args[["tag"]] <- NULL
message(paste0(tag, paste(strwrap(
args, indent = indent, exdent = exdent
), collapse = collapse)), appendLF = appendLF, domain = domain)
}
.warning <- function(...) {
# Function to use the 'warning' R function with our custom settings
# Default: no call information, indent to 0, exdent to 3,
# collapse to \n
args <- list(...)
## In case we need to specify warning arguments
if (!is.null(args[["call."]])) {
call <- args[["call."]]
} else {
## Default: don't show info about the call where the warning came up
call <- FALSE
}
if (!is.null(args[["immediate."]])) {
immediate <- args[["immediate."]]
} else {
## Default value in warning function
immediate <- FALSE
}
if (!is.null(args[["noBreaks."]])) {
noBreaks <- args[["noBreaks."]]
} else {
## Default value warning function
noBreaks <- FALSE
}
if (!is.null(args[["domain"]])) {
domain <- args[["domain"]]
} else {
## Default value warning function
domain <- NULL
}
args[["call."]] <- NULL
args[["immediate."]] <- NULL
args[["noBreaks."]] <- NULL
args[["domain"]] <- NULL
## To modify strwrap indent and exdent arguments
if (!is.null(args[["indent"]])) {
indent <- args[["indent"]]
} else {
indent <- 0
}
if (!is.null(args[["exdent"]])) {
exdent <- args[["exdent"]]
} else {
exdent <- 3
}
args[["indent"]] <- NULL
args[["exdent"]] <- NULL
## To modify paste collapse argument
if (!is.null(args[["collapse"]])) {
collapse <- args[["collapse"]]
} else {
collapse <- "\n!"
}
args[["collapse"]] <- NULL
## Warning tag
if (!is.null(args[["tag"]])) {
tag <- args[["tag"]]
} else {
tag <- "! Warning: "
}
args[["tag"]] <- NULL
warning(paste0(tag, paste(strwrap(
args, indent = indent, exdent = exdent
), collapse = collapse)), call. = call, immediate. = immediate,
noBreaks. = noBreaks, domain = domain)
}
# Function to permute arrays of non-atomic elements (e.g. POSIXct)
.aperm2 <- function(x, new_order) {
y <- array(1:length(x), dim = dim(x))
y <- aperm(y, new_order)
old_dims <- dim(x)
x <- x[as.vector(y)]
dim(x) <- old_dims[new_order]
x
}
# This function is a helper for the function .MergeArrays.
# It expects as inputs two named numeric vectors, and it extends them
# with dimensions of length 1 until an ordered common dimension
# format is reached.
.MergeArrayDims <- function(dims1, dims2) {
new_dims1 <- c()
new_dims2 <- c()
while (length(dims1) > 0) {
if (names(dims1)[1] %in% names(dims2)) {
pos <- which(names(dims2) == names(dims1)[1])
dims_to_add <- rep(1, pos - 1)
if (length(dims_to_add) > 0) {
names(dims_to_add) <- names(dims2[1:(pos - 1)])
}
new_dims1 <- c(new_dims1, dims_to_add, dims1[1])
new_dims2 <- c(new_dims2, dims2[1:pos])
dims1 <- dims1[-1]
dims2 <- dims2[-c(1:pos)]
} else {
new_dims1 <- c(new_dims1, dims1[1])
new_dims2 <- c(new_dims2, 1)
names(new_dims2)[length(new_dims2)] <- names(dims1)[1]
dims1 <- dims1[-1]
}
}
if (length(dims2) > 0) {
dims_to_add <- rep(1, length(dims2))
names(dims_to_add) <- names(dims2)
new_dims1 <- c(new_dims1, dims_to_add)
new_dims2 <- c(new_dims2, dims2)
}
list(new_dims1, new_dims2)
}
# This function takes two named arrays and merges them, filling with
# NA where needed.
# dim(array1)
# 'b' 'c' 'e' 'f'
# 1 3 7 9
# dim(array2)
# 'a' 'b' 'd' 'f' 'g'
# 2 3 5 9 11
# dim(.MergeArrays(array1, array2, 'b'))
# 'a' 'b' 'c' 'e' 'd' 'f' 'g'
# 2 4 3 7 5 9 11
.MergeArrays <- function(array1, array2, along) {
if (!(identical(names(dim(array1)), names(dim(array2))) &&
identical(dim(array1)[-which(names(dim(array1)) == along)],
dim(array2)[-which(names(dim(array2)) == along)]))) {
new_dims <- .MergeArrayDims(dim(array1), dim(array2))
dim(array1) <- new_dims[[1]]
dim(array2) <- new_dims[[2]]
for (j in 1:length(dim(array1))) {
if (names(dim(array1))[j] != along) {
if (dim(array1)[j] != dim(array2)[j]) {
if (which.max(c(dim(array1)[j], dim(array2)[j])) == 1) {
na_array_dims <- dim(array2)
na_array_dims[j] <- dim(array1)[j] - dim(array2)[j]
na_array <- array(dim = na_array_dims)
array2 <- abind(array2, na_array, along = j)
names(dim(array2)) <- names(na_array_dims)
} else {
na_array_dims <- dim(array1)
na_array_dims[j] <- dim(array2)[j] - dim(array1)[j]
na_array <- array(dim = na_array_dims)
array1 <- abind(array1, na_array, along = j)
names(dim(array1)) <- names(na_array_dims)
}
}
}
}
}
array1 <- abind(array1, array2, along = which(names(dim(array1)) == along))
names(dim(array1)) <- names(dim(array2))
array1
}