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feat: read_*_data() functions do not download files anymore
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@ahasverus
ahasverus committed Feb 15, 2024
1 parent bc49107 commit 4e377b1
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Showing 6 changed files with 78 additions and 166 deletions.
36 changes: 11 additions & 25 deletions R/read_cpr_north_data.R
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
#' @rdname read_data
#' @export

read_cpr_north_data <- function(path = ".",
version = options()$"forcis_version",
check_for_update = options()$"check_for_update",
overwrite = FALSE, timeout = 60) {
read_cpr_north_data <- function(
path = ".",
version = options()$"forcis_version",
check_for_update = options()$"check_for_update") {

## Check args ----

Expand All @@ -21,38 +21,24 @@ read_cpr_north_data <- function(path = ".",
version <- set_version(version, ask = check_for_update)


## Build outputs directory ----
## Check local database ----

path <- file.path(path, "forcis-db", paste0("version-", version))

if (!dir.exists(path)) {
dir.create(path, recursive = TRUE)
stop("The directory '", path, "' does not exist. Please check the ",
"argument 'path' or use the function 'download_forcis_db()'.",
call. = FALSE)
}


## Download file (if required) ----
## Check file ----

file_name <- list.files(path, pattern = cpr_north_filename())

if (!length(file_name)) {

forcis_meta <- get_version_info(version = version)
forcis_files <- forcis_meta$"files"

pos <- grep(cpr_north_filename(), forcis_files$"key")

if (length(pos) == 1) {

download_file(url = forcis_files[pos, "links"]$"self",
path = path,
file = forcis_files[pos, "key"],
overwrite = overwrite,
timeout = timeout)

} else {

stop("Unable to download the 'CPR North' dataset", call. = FALSE)
}
stop("The North CPR dataset does not exist. Please use the function ",
"'download_forcis_db()'.", call. = FALSE)
}


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36 changes: 11 additions & 25 deletions R/read_cpr_south_data.R
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
#' @rdname read_data
#' @export

read_cpr_south_data <- function(path = ".",
version = options()$"forcis_version",
check_for_update = options()$"check_for_update",
overwrite = FALSE, timeout = 60) {
read_cpr_south_data <- function(
path = ".",
version = options()$"forcis_version",
check_for_update = options()$"check_for_update") {

## Check args ----

Expand All @@ -21,38 +21,24 @@ read_cpr_south_data <- function(path = ".",
version <- set_version(version, ask = check_for_update)


## Build outputs directory ----
## Check local database ----

path <- file.path(path, "forcis-db", paste0("version-", version))

if (!dir.exists(path)) {
dir.create(path, recursive = TRUE)
stop("The directory '", path, "' does not exist. Please check the ",
"argument 'path' or use the function 'download_forcis_db()'.",
call. = FALSE)
}


## Download file (if required) ----
## Check file ----

file_name <- list.files(path, pattern = cpr_south_filename())

if (!length(file_name)) {

forcis_meta <- get_version_info(version = version)
forcis_files <- forcis_meta$"files"

pos <- grep(cpr_south_filename(), forcis_files$"key")

if (length(pos) == 1) {

download_file(url = forcis_files[pos, "links"]$"self",
path = path,
file = forcis_files[pos, "key"],
overwrite = overwrite,
timeout = timeout)

} else {

stop("Unable to download the 'CPR South' dataset", call. = FALSE)
}
stop("The South CPR dataset does not exist. Please use the function ",
"'download_forcis_db()'.", call. = FALSE)
}


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56 changes: 21 additions & 35 deletions R/read_plankton_nets_data.R
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Original file line number Diff line number Diff line change
@@ -1,25 +1,25 @@
#' Import FORCIS data
#' Read FORCIS data
#'
#' @description
#' These functions import one specific `csv` file of the FORCIS database
#' (see below) stored in the folder `path`. If the `csv` file does not exist
#' it will be downloaded from Zenodo (\url{https://zenodo.org/record/7936568}).
#' These functions read one specific `csv` file of the FORCIS database
#' (see below) stored in the folder `path`. The function [download_forcis_db()]
#' must be used first to store locally the database.
#'
#' @param path a `character` of length 1. The folder in which the FORCIS
#' database has been (or will be) saved.
#' database has been saved.
#'
#' @inheritParams download_forcis_db
#'
#' @details
#'
#' - `read_plankton_nets_data()` imports the FORCIS plankton nets data
#' - `read_pump_data()` imports the FORCIS pump data
#' - `read_cpr_north_data()` imports the FORCIS CPR North data
#' - `read_cpr_south_data()` imports the FORCIS CPR South data
#' - `read_sediment_trap_data()` imports the FORCIS sediment traps data
#' - `read_plankton_nets_data()` reads the FORCIS plankton nets data
#' - `read_pump_data()` reads the FORCIS pump data
#' - `read_cpr_north_data()` reads the FORCIS CPR North data
#' - `read_cpr_south_data()` reads the FORCIS CPR South data
#' - `read_sediment_trap_data()` reads the FORCIS sediment traps data
#'
#' @return A `data.frame`. See \url{https://zenodo.org/record/7390792} for a
#' preview of the dataset.
#' preview of the datasets.
#'
#' @seealso [download_forcis_db()] to download the complete FORCIS database.
#'
Expand All @@ -32,9 +32,9 @@ NULL
#' @export

read_plankton_nets_data <- function(
path = ".", version = options()$"forcis_version",
check_for_update = options()$"check_for_update",
overwrite = FALSE, timeout = 60) {
path = ".",
version = options()$"forcis_version",
check_for_update = options()$"check_for_update") {

## Check args ----

Expand All @@ -51,38 +51,24 @@ read_plankton_nets_data <- function(
version <- set_version(version, ask = check_for_update)


## Build outputs directory ----
## Check local database ----

path <- file.path(path, "forcis-db", paste0("version-", version))

if (!dir.exists(path)) {
dir.create(path, recursive = TRUE)
stop("The directory '", path, "' does not exist. Please check the ",
"argument 'path' or use the function 'download_forcis_db()'.",
call. = FALSE)
}


## Download file (if required) ----
## Check file ----

file_name <- list.files(path, pattern = plankton_net_filename())

if (!length(file_name)) {

forcis_meta <- get_version_info(version = version)
forcis_files <- forcis_meta$"files"

pos <- grep(plankton_net_filename(), forcis_files$"key")

if (length(pos) == 1) {

download_file(url = forcis_files[pos, "links"]$"self",
path = path,
file = forcis_files[pos, "key"],
overwrite = overwrite,
timeout = timeout)

} else {

stop("Unable to download the 'Plankton nets' dataset", call. = FALSE)
}
stop("The Plankton net dataset does not exist. Please use the function ",
"'download_forcis_db()'.", call. = FALSE)
}


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36 changes: 11 additions & 25 deletions R/read_pump_data.R
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
#' @rdname read_data
#' @export

read_pump_data <- function(path = ".",
version = options()$"forcis_version",
check_for_update = options()$"check_for_update",
overwrite = FALSE, timeout = 60) {
read_pump_data <- function(
path = ".",
version = options()$"forcis_version",
check_for_update = options()$"check_for_update") {

## Check args ----

Expand All @@ -21,38 +21,24 @@ read_pump_data <- function(path = ".",
version <- set_version(version, ask = check_for_update)


## Build outputs directory ----
## Check local database ----

path <- file.path(path, "forcis-db", paste0("version-", version))

if (!dir.exists(path)) {
dir.create(path, recursive = TRUE)
stop("The directory '", path, "' does not exist. Please check the ",
"argument 'path' or use the function 'download_forcis_db()'.",
call. = FALSE)
}


## Download file (if required) ----
## Check file ----

file_name <- list.files(path, pattern = pump_filename())

if (!length(file_name)) {

forcis_meta <- get_version_info(version = version)
forcis_files <- forcis_meta$"files"

pos <- grep(pump_filename(), forcis_files$"key")

if (length(pos) == 1) {

download_file(url = forcis_files[pos, "links"]$"self",
path = path,
file = forcis_files[pos, "key"],
overwrite = overwrite,
timeout = timeout)

} else {

stop("Unable to download the 'Pumps' dataset", call. = FALSE)
}
stop("The Pump dataset does not exist. Please use the function ",
"'download_forcis_db()'.", call. = FALSE)
}


Expand Down
31 changes: 8 additions & 23 deletions R/read_sediment_trap_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,7 @@

read_sediment_trap_data <- function(
path = ".", version = options()$"forcis_version",
check_for_update = options()$"check_for_update",
overwrite = FALSE, timeout = 60) {
check_for_update = options()$"check_for_update") {

## Check args ----

Expand All @@ -21,38 +20,24 @@ read_sediment_trap_data <- function(
version <- set_version(version, ask = check_for_update)


## Build outputs directory ----
## Check local database ----

path <- file.path(path, "forcis-db", paste0("version-", version))

if (!dir.exists(path)) {
dir.create(path, recursive = TRUE)
stop("The directory '", path, "' does not exist. Please check the ",
"argument 'path' or use the function 'download_forcis_db()'.",
call. = FALSE)
}


## Download file (if required) ----
## Check file ----

file_name <- list.files(path, pattern = sediment_trap_filename())

if (!length(file_name)) {

forcis_meta <- get_version_info(version = version)
forcis_files <- forcis_meta$"files"

pos <- grep(sediment_trap_filename(), forcis_files$"key")

if (length(pos) == 1) {

download_file(url = forcis_files[pos, "links"]$"self",
path = path,
file = forcis_files[pos, "key"],
overwrite = overwrite,
timeout = timeout)

} else {

stop("Unable to download the 'Sediment traps' dataset", call. = FALSE)
}
stop("The Sediment trap dataset does not exist. Please use the function ",
"'download_forcis_db()'.", call. = FALSE)
}


Expand Down
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