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script_management.R
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script_management.R
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# Copyright 2021-2023 Louis Héraut (louis.heraut@inrae.fr)*1,
# Éric Sauquet (eric.sauquet@inrae.fr)*1
#
# *1 INRAE, France
#
# This file is part of Explore2 R toolbox.
#
# Explore2 R toolbox is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# Explore2 R toolbox is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Explore2 R toolbox.
# If not, see <https://www.gnu.org/licenses/>.
## 1. MANAGEMENT OF DATA ______________________________________________
if (!read_tmp & !delete_tmp) {
if ('save_data' %in% to_do) {
print("### Saving data")
print(paste0("Save extracted data and metadata in ",
paste0(saving_format, collapse=", ")))
today_resdir_tmp = today_resdir
pattern = "data[_].*[.]fst"
if (!(file.exists(today_resdir_tmp))) {
dir.create(today_resdir_tmp, recursive=TRUE)
}
data_paths = list.files(tmppath,
pattern=pattern,
full.names=TRUE)
data_files = gsub("[_][_]", "_", basename(data_paths))
if ("data" %in% var2save) {
for (format in saving_format) {
if (length(saving_format) > 1) {
today_resdir_format_tmp =
file.path(today_resdir_tmp,
toupper(format))
if (!(file.exists(today_resdir_format_tmp))) {
dir.create(today_resdir_format_tmp,
recursive=TRUE)
}
} else {
today_resdir_format_tmp = today_resdir_tmp
}
# file.copy(data_paths,
# file.path(today_resdir_tmp, data_files))
write_tibble(data,
filedir=today_resdir_format_tmp,
filename=paste0("data",
".", format))
}
}
for (i in 1:length(extract_data)) {
extract = extract_data[[i]]
dirname = paste0("dataEX_", data_dir_to_use, "_",
extract$name)
filename = paste0(dirname, ".fst")
if (file.exists(file.path(tmppath, dirname)) |
file.exists(file.path(tmppath, filename))) {
if ("meta" %in% var2save) {
meta = read_tibble(filedir=tmppath,
filename=paste0(
"meta_",
data_dir_to_use,
".fst"))
}
if ("metaEX" %in% var2save) {
metaEX = read_tibble(filedir=tmppath,
filename=paste0(
"metaEX_",
data_dir_to_use, "_",
extract$name,
".fst"))
}
if ("dataEX" %in% var2save) {
dataEX = read_tibble(filedir=tmppath,
filename=paste0(
"dataEX_",
data_dir_to_use, "_",
extract$name,
".fst"))
}
if ("trendEX" %in% var2save) {
trendEX = read_tibble(filedir=tmppath,
filename=paste0(
"trendEX_",
data_dir_to_use, "_",
extract$name,
".fst"))
}
} else {
next
}
for (format in saving_format) {
if (length(saving_format) > 1) {
today_resdir_format_tmp =
file.path(today_resdir_tmp,
toupper(format))
if (!(file.exists(today_resdir_format_tmp))) {
dir.create(today_resdir_format_tmp,
recursive=TRUE)
}
} else {
today_resdir_format_tmp = today_resdir_tmp
}
if ("meta" %in% var2save) {
write_tibble(meta,
filedir=today_resdir_format_tmp,
filename=paste0("meta_",
data_dir_to_use,
".", format))
}
if ("metaEX" %in% var2save) {
write_tibble(metaEX,
filedir=today_resdir_format_tmp,
filename=paste0("metaEX_",
data_dir_to_use, "_",
extract$name,
".", format))
}
if ("dataEX" %in% var2save) {
write_tibble(dataEX,
filedir=today_resdir_format_tmp,
filename=paste0("dataEX_",
data_dir_to_use, "_",
extract$name,
".", format))
}
if ("trendEX" %in% var2save) {
write_tibble(trendEX,
filedir=today_resdir_format_tmp,
filename=paste0("trendEX_",
data_dir_to_use, "_",
extract$name,
".", format))
}
}
if (exists("meta")) {
rm ("meta")
gc()
}
if (exists("metaEX")) {
rm ("metaEX")
gc()
}
if (exists("dataEX")) {
rm ("dataEX")
gc()
}
if (exists("trendEX")) {
rm ("trendEX")
gc()
}
}
}
if ('read_saving' %in% to_do) {
print("### Reading saving")
print(paste0("Reading extracted data and metadata in ",
read_saving))
read_saving_tmp = file.path(read_saving)
if (length(saving_format) > 1) {
read_saving_tmp = file.path(read_saving, "FST")
}
for (i in 1:length(extract_data)) {
extract = extract_data[[i]]
Paths = list.files(file.path(resdir,
read_saving_tmp),
include.dirs=TRUE,
full.names=TRUE)
pattern = var2search
pattern = paste0("(", paste0(pattern,
collapse=")|("), ")")
if (extract$simplify) {
pattern = gsub("dataEX",
paste0("dataEX[_]",
gsub("[_]", "[_]",
data_dir_to_use),
"[_]",
gsub("[_]", "[_]",
extract$name),
"[.]"),
pattern)
} else {
pattern = gsub("dataEX",
paste0("dataEX[_]",
gsub("[_]", "[_]",
data_dir_to_use),
"[_]",
gsub("[_]", "[_]",
extract$name),
"$"),
pattern)
}
pattern = gsub("metaEX",
paste0("metaEX[_]",
gsub("[_]", "[_]",
data_dir_to_use),
"[_]",
gsub("[_]", "[_]",
extract$name),
"[.]"),
pattern)
pattern = gsub("trendEX", paste0("trendEX[_]",
gsub("[_]", "[_]",
data_dir_to_use),
"[_]",
gsub("[_]", "[_]",
extract$name),
"[.]"),
pattern)
Paths = Paths[grepl(pattern, Paths)]
Paths = Paths[grepl("[.]fst", Paths) | !grepl("?[.]", Paths)]
Paths[!grepl("[.]", Paths)] =
paste0(Paths[!grepl("[.]", Paths)], ".fst")
Filenames = gsub("^.*[/]+", "", Paths)
Filenames = gsub("[.].*$", "", Filenames)
nFile = length(Filenames)
for (i in 1:nFile) {
print(paste0(Filenames[i], " reads in ", Paths[i]))
assign(Filenames[i],
read_tibble(filepath=Paths[i]))
}
}
}
} else {
if (read_tmp) {
print("### Reading tmp")
print(paste0("Reading tmp data in ", tmppath))
Paths = list.files(tmppath,
pattern=paste0("(",
paste0(var2search,
collapse=")|("),
")"),
include.dirs=TRUE,
full.names=TRUE)
Paths = Paths[grepl("[.]fst", Paths) | !grepl("?[.]", Paths)]
Paths[!grepl("[.]", Paths)] =
paste0(Paths[!grepl("[.]", Paths)], ".fst")
Filenames = gsub("^.*[/]+", "", Paths)
Filenames = gsub("[.].*$", "", Filenames)
nFile = length(Filenames)
for (i in 1:nFile) {
print(paste0(Filenames[i], " reads in ", Paths[i]))
assign(Filenames[i], read_tibble(filepath=Paths[i]))
}
read_tmp = FALSE
}
if (delete_tmp) {
print("### Deleting tmp")
if (file.exists(tmppath)) {
unlink(tmppath, recursive=TRUE)
}
delete_tmp = FALSE
}
}