diff --git a/.Rbuildignore b/.Rbuildignore index 0d08781..8f484ee 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -2,3 +2,10 @@ ^Makefile$ ^_pkgdown.yml$ ^docs$ +^contact.md +^pkgdown +^test.R + +^vignettes/datasets.Rmd +^vignettes/metadata.Rmd +^vignettes/stationdata.Rmd diff --git a/DESCRIPTION b/DESCRIPTION index b0b0762..b9eb676 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,15 +1,17 @@ Package: gsdata Type: Package -Title: Accessing Data from Geosphere Austria -Version: 0.0-6 -Date: 2023-08-03 +Title: Interface to the GeoSphere Austria DataHub API (Data Access) +Version: 0.0-7 +Date: 2024-01-23 Authors@R: person(given = "Reto", family = "Stauffer", role = c("cre", "aut"), email = "reto.stauffer@uibk.ac.at", comment = c(ORCID = "0000-0002-3798-5507")) Maintainer: Reto Stauffer Depends: httr, zoo, sf, parsedate -Description: Package to download data from the Geosphere data hub (formerly known as ZAMG; Austrian National Weather Service). Currently solely allows to download station data (no gridded data). More details about the data sets can be found on as well as in the API documentation available via . -License: GPL-2 | GPL-3 +Suggests: utils, ncdf4, stars, knitr, rmarkdown, tinytest +Description: Package to download data from the Geosphere data hub (Austrian National Weather Service) which is the data provider. Currently solely allows to download station data (no gridded data). More details about the data sets can be found on as well as in the API documentation available via . +License: GPL-2 +VignetteBuilder: knitr RoxygenNote: 7.2.3 Roxygen: list(markdown = TRUE) diff --git a/LICENSE b/LICENSE deleted file mode 100644 index f288702..0000000 --- a/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. By contrast, -the GNU General Public License is intended to guarantee your freedom to -share and change all versions of a program--to make sure it remains free -software for all its users. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/Makefile b/Makefile index ed698e9..fd5c27f 100644 --- a/Makefile +++ b/Makefile @@ -12,10 +12,14 @@ document: docs: Rscript -e "pkgdown::build_site()" +.PHONY: vignettes +vignettes: + Rscript -e "devtools::build_vignettes()" + install: document Rscript -e "devtools::install()" -check: document +devcheck: document Rscript -e "devtools::check()" test: install @@ -26,3 +30,14 @@ testwarn: install coverage: install Rscript -e 'covr::report(covr::package_coverage(), file = "../coverage.html")' +# --------------------------------------------------- +# R CMD build and check (--as-cran) +# --------------------------------------------------- +packageversion:=$(shell cat DESCRIPTION | egrep Version | sed 's/Version://g') + +build: document + cd ../ && \ + R CMD build --no-build-vignettes gsdata +check: build + cd ../ && \ + R CMD check --as-cran gsdata_$(shell printf "%s"${packageversion}).tar.gz diff --git a/NAMESPACE b/NAMESPACE index 5452aa0..bd1e155 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,12 +8,14 @@ export(gs_stationdata) export(gs_temporal_interval) importFrom(httr,GET) importFrom(httr,content) +importFrom(httr,http_status) importFrom(httr,status_code) importFrom(parsedate,parse_iso_8601) importFrom(sf,st_as_sf) importFrom(sf,st_point) importFrom(utils,head) importFrom(utils,tail) +importFrom(zoo,coredata) importFrom(zoo,index) importFrom(zoo,plot.zoo) importFrom(zoo,zoo) diff --git a/R/datasets.R b/R/datasets.R index 65b6755..a44740d 100644 --- a/R/datasets.R +++ b/R/datasets.R @@ -37,14 +37,16 @@ #' #' Can be combined (settinb both \code{type} and \code{mode}). #' -#' @importFrom httr GET content status_code #' @author Reto Stauffer #' @export gs_datasets <- function(type = "station", mode = NULL, version = 1L, config = list(), verbose = FALSE) { - stopifnot("argument 'verbose' must be logical TRUE or FALSE" = isTRUE(verbose) || isFALSE(verbose)) + stopifnot("argument 'verbose' must be logical TRUE or FALSE" = + isTRUE(verbose) || isFALSE(verbose)) stopifnot("argument 'config' must be a (named) list" = is.list(config)) - stopifnot("argument 'type' must be NULL or a character string" = is.null(type) || (is.character(type) & length(type) == 1L)) - stopifnot("argument 'mode' must be NULL or a character string" = is.null(mode) || (is.character(mode) & length(mode) == 1L)) + stopifnot("argument 'type' must be NULL or a character string" = + is.null(type) || (is.character(type) & length(type) == 1L)) + stopifnot("argument 'mode' must be NULL or a character string" = + is.null(mode) || (is.character(mode) & length(mode) == 1L)) # Parsing 'query' arguments (if any) # Get base URL; performs version sanity check @@ -54,41 +56,26 @@ gs_datasets <- function(type = "station", mode = NULL, version = 1L, config = li # Query args query <- list(); query$type <- type; query$mode <- mode - # Verbosity - if (verbose) - message(sprintf("Calling: %s%s%s", URL, - if (!length(query)) "" else "?", - if (!length(query)) "" else paste(paste(names(query), query, sep = "="), collapse = "&"))) - - # Requesting data - req <- GET(URL, config = config, query = query) - if (!status_code(req) == 200) { - tmp <- try(content(req)) - if (is.list(tmp) && !is.null(tmp$detail[[1]]$msg)) { - stop(tmp$detail[[1]]$msg) - } else { - stop("HTTP request error: got status code", status_code(req)) - } - } - content <- content(req) - keys <- unique(unlist(lapply(content, names))) + # Calling API + res <- API_GET(URL, config = config, query = query, verbose = verbose) + keys <- unique(unlist(lapply(res, names))) # Splitting up the path to get the information - tmp <- strsplit(sub("^\\/", "", names(content)), "/") + tmp <- strsplit(sub("^\\/", "", names(res)), "/") if (!all(sapply(tmp, length))) stop("problems decoding the path argument (expected three-part-path)") # Else setting up results data.frame - res <- data.frame(type = sapply(tmp, function(x) x[1]), - mode = sapply(tmp, function(x) x[2]), - resource_id = sapply(tmp, function(x) x[3])) + rval <- data.frame(type = sapply(tmp, function(x) x[1]), + mode = sapply(tmp, function(x) x[2]), + resource_id = sapply(tmp, function(x) x[3])) fn <- function(x, k) if (is.character(x[[k]])) x[[k]] else paste(x[[k]], collapse = "|") for (k in keys) { kn <- if (k == "type") "data_format" else k # New name to not overwrite 'type' - res[[kn]] <- unname(sapply(content, fn, k = k)) + rval[[kn]] <- unname(sapply(res, fn, k = k)) } # Return data.frame - return(res) + return(rval) } diff --git a/R/gsdata.R b/R/gsdata.R new file mode 100644 index 0000000..5dc17c5 --- /dev/null +++ b/R/gsdata.R @@ -0,0 +1,66 @@ + +#' \code{gsdata}: Interface to the GeoSphere Austria DataHub API (Data Access) +#' +#' This package allows convenient access to data provided by GeoSphere Austria +#' (Austrias federal agency for geology, geophysics, climatology and +#' meteorology) via their data API which exists since around mid 2023. +#' +#' The API not only provides access to station data (the one thing currently +#' covered by this package; will be extended) but also access to spatial +#' data; a catalogue which has been extended over and over again over the past +#' 10 months. Details about all available data sets and their temporal and +#' spatial extent can be found on their website: +#' +#' \itemize{ +#' \item +#' } +#' +#' @section Data request limit: +#' +#' The API has a request limit; a limit to how much data one is allowed +#' to retrieve in one API request. Details on the current limit can be found +#' in the [GeoSphere Dataset API Documentation](https://dataset.api.hub.geosphere.at/v1/docs/user-guide/request_size_limit.html). +#' +#' This package internally tries to estimate the request size and split the +#' request into multiple batches in case one single request would (likely) +#' exceed these limits. +#' +#' Thus, one single call to e.g., \code{gs_stationdata()} can trigger multiple +#' API calls. If used without `expert = TRUE` two initial calls are made to +#' check if the data set requested does exist, and that the +#' stations and parameters requested exist in this data set. If the data request +#' needs to be split in addition, this can cause a series of calls to the API +#' which also has a limit on number of requests per time. +#' +#' In the worst case this causes a temporary ban (timeout due to too many requests) +#' from the servers. One way around is to limit the number of requests per time, +#' more details about this in the next section. +#' +#' +#' @section Cooldown time/limiting number of requests per time: +#' +#' +#' Note that each function call can result in multiple API requests which can +#' lead to a timeout (too many requests). To avoid running into timeout issues: +#' +#' \itemize{ +#' \item use \code{expert = TURUE} where possible as it +#' lowers the number of calls to the api. +#' \item request data for multiple stations at once, especially +#' when requesting short time periods/few parameters as, in the best case, +#' all data can be retrieved on one single call (if below estimated +#' data request limit). +#' \item wait between requests using e.g., \code{Sys.sleep(...)}. +#' \item or use the packages own 'cooldown' option. By default, +#' a cooldown time of \code{0.1} seconds is used (the minimum +#' time between two requests. You can set a custom cooldown time +#' via \code{options('gsdata.cooldown' = 1)}. Will overwrite the +#' default and ensure that there will be at least one second +#' between consecutive API calls. If you have no time critical +#' requests this is a good way to be nice to the data provider! +#' } +#' +#' @docType package +#' @name gsdata +"_PACKAGE" + diff --git a/R/helperfunctions.R b/R/helperfunctions.R index 3a4928e..6521e8f 100644 --- a/R/helperfunctions.R +++ b/R/helperfunctions.R @@ -75,3 +75,128 @@ gs_temporal_interval <- function(resource_id) { return(res) } + + + +#' Show HTTP Error Status and Terminate +#' +#' This function is called whenever \code{httr::GET} returns an +#' http status code out of the \code{200} range (success). +#' Shows \code{\link[http]{http_status()}} code information alongside +#' with additional messages returned by the API (if any). +#' +#' @param scode numeric, http status code. +#' @param xtra \code{NULL} or named list with additional information. +#' +#' @return No return, will terminate R. +#' +#' @author Reto Stauffer +# Show http_status message if possible. +show_http_status_and_terminate <- function(scode, xtra = NULL) { + + stopifnot(is.numeric(scode), length(scode) == 1) + if (scode %/% 100 == 2) return(NULL) + cat('---\n') + + info <- tryCatch(http_status(scode), + error = function(x) NULL) + + # Depending on the status code these are somewhat redundant + if (!is.null(xtra)) + xtra <- paste(c(" status returned by API:", + sprintf(" %-20s %s", sprintf("%s:", names(xtra)), xtra)), + collapse = "\n") + if (!is.null(info)) + info <- paste(c(" http_status description:", + sprintf(" %-20s %s", sprintf("%s:", names(info)), info)), + collapse = "\n") + + if (is.null(info) & is.null(xtra)) { + stop("HTTP request error: server returned status code ", scode) + } else { + stop(paste("HTTP request error", xtra, info, sep = "\n")) + } +} + +#' Handling API Calls +#' +#' Small helper function to handle http requests to the API. +#' +#' @param URL the URL to be called. +#' @param config \code{NULL} or \code{list}, forwarded to \code{httr::GET}. +#' @param query \code{NULL} or \code{list}, forwarded to \code{httr::GET}. +#' @param expected_class \code{NULL} or character vector. If set, it is checked +#' if the returned object is of this class. If not, a warning will be thrown +#' (no error). +#' @param verbose logical, shows some additional information if \code{TRUE}. +#' +#' @return Returns the object we get from \code{httr::content()} after a successful +#' API call. If an error is detected, an error with additional details will be displayed. +#' +#' @importFrom httr GET status_code content http_status +#' @author Reto Stauffer +API_GET <- function(URL, config = NULL, query = NULL, + expected_class = NULL, verbose = FALSE) { + # Checking URL + URL <- as.character(URL)[[1]] + stopifnot("argument `URL` is invalid" = + grepl("^https:\\/\\/dataset.api.hub.geosphere.at", URL)) + + stopifnot("argument `config` must be NULL or a list" = + is.null(config) || is.list(config)) + stopifnot("argument `query` must be NULL or a list" = + is.null(query) || is.list(query)) + stopifnot("argument `expected` must be NULL or character" = + is.null(expected_class) || is.character(expected_class)) + stopifnot("argument `verbose` must be logical TRUE or FALSE" = + isTRUE(verbose) || isFALSE(verbose)) + + + # Checking and executing cooldown + gsdata_lastcall <- getOption("gsdata.lastcall", default = Sys.time() - 1); # 1s ago + gsdata_cooldown <- getOption("gsdata.cooldown", default = .1) # cooldown in secs + # Ensure positive numeric, if there is an error or any warning we reset to default .1 + gsdata_cooldown <- tryCatch(max(0, as.numeric(gsdata_cooldown)), + warning = function(x) .1, + error = function(x) .1) + sleep_time <- gsdata_cooldown - as.numeric(Sys.time() - gsdata_lastcall, units = "secs") + if (sleep_time > 0.1) { + if (verbose) message(sprintf("Cooldown, waiting for %.3f seconds", sleep_time)) + Sys.sleep(sleep_time) + } + + + if (verbose) { + msgq <- if (is.list(query)) { + paste0("?", paste(paste(names(query), query, sep = "="), collapse = "&")) + } else { "" } + message(sprintf("Calling: %s%s", URL, msgq)) + } + + # Requesting data + req <- GET(URL, config = config, query = query) + options("gsdata.lastcall" = Sys.time()) # Updating last call + + if (!status_code(req) %/% 100 == 2) { + # Trying to read the response and see if the API answered + # with an error message (error details). If so, that will be + # shown, else a more generic error will be displayed. + tmp <- tryCatch(content(req), error = function(x) NULL) + show_http_status_and_terminate(status_code(req), tmp) + } + + # Else extracting the content + content <- content(req) + + # If a certain class is expected check and throw a warning + # if the object is not of the correct class. + if (!is.null(expected_class)) { + if (!inherits(content, expected_class)) { + warning("expected returned object from HTTP request to be of class ", + paste(expected_class, collapse = ", "), " but it is of ", + paste(class(content), collapse = ", ")) + } + } + + return(content) +} diff --git a/R/metadata.R b/R/metadata.R index 6089640..b68c62a 100644 --- a/R/metadata.R +++ b/R/metadata.R @@ -8,6 +8,10 @@ #' @param version integer, API version (defaults to \code{1L}). #' @param config empty list by default; can be a named list to be fowrarded #' to the \code{httr::GET} request if needed. +#' @param expert logical, defaults to \code{FALSE}. If \code{TRUE} the script will not +#' check if the input arguments are valid. May result in unsuccessful requests +#' but increases the speed as \code{gs_datasets()} does not have to be +#' called (one less API request). #' @param verbose logical, if set \code{TRUE} some more output will be produced. #' #' @return Named list with a series of information about the dataset. @@ -50,66 +54,69 @@ #' #' @author Reto Stauffer #' @export -#' @importFrom httr GET status_code content #' @importFrom sf st_as_sf #' @importFrom parsedate parse_iso_8601 -gs_metadata <- function(mode, resource_id, type = NULL, version = 1L, config = list(), verbose = FALSE) { +gs_metadata <- function(mode, resource_id, type = NULL, version = 1L, config = list(), expert = FALSE, verbose = FALSE) { # Getting available dataset dynamically; used to perform 'sanity check' # (whether or not the defined mode/resource_id is a valid identifier) - stopifnot("argument 'mode' must be character of length 1" = is.character(mode) && length(mode) == 1) - stopifnot("argument 'resource_id' must be character of length 1" = is.character(resource_id) && length(resource_id) == 1) - stopifnot("argument 'type' must be NULL or character of length 1" = is.null(type) || (is.character(type) && length(type) == 1L)) - stopifnot("argument 'verbose' must be logical TRUE or FALSE" = isTRUE(verbose) || isFALSE(verbose)) + stopifnot("argument 'mode' must be character of length 1" = + is.character(mode) && length(mode) == 1) + stopifnot("argument 'resource_id' must be character of length 1" = + is.character(resource_id) && length(resource_id) == 1) + stopifnot("argument 'type' must be NULL or character of length 1" = + is.null(type) || (is.character(type) && length(type) == 1L)) + stopifnot("argument 'expert' must be logical TRUE or FALSE" = + isTRUE(expert) || isFALSE(expert)) + stopifnot("argument 'verbose' must be logical TRUE or FALSE" = + isTRUE(verbose) || isFALSE(verbose)) - dataset <- gs_datasets(version = version) - mode <- match.arg(mode, unique(dataset$mode)) - resource_id <- match.arg(resource_id, unique(dataset$resource_id)) - if (!is.null(type)) type <- match.arg(type, unique(dataset$type)) + # Check if mode/resource_id is a valid combination + if (!expert) { + dataset <- gs_datasets(version = version) + mode <- match.arg(mode, unique(dataset$mode)) + resource_id <- match.arg(resource_id, unique(dataset$resource_id)) + if (!is.null(type)) type <- match.arg(type, unique(dataset$type)) - # Checking available resource ids. Enforcing one of the types defined below - dataset <- dataset[dataset$mode == mode & dataset$resource_id == resource_id, ] - if (!is.null(type)) dataset <- dataset[dataset$type == type, ] + # Checking available resource ids. Enforcing one of the types defined below + dataset <- dataset[dataset$mode == mode & dataset$resource_id == resource_id, ] + if (!is.null(type)) dataset <- dataset[dataset$type == type, ] - # More than one match? - if (nrow(dataset) > 1L && is.null(type)) { - stop("Found ", nrow(dataset), " datasets matching the input arguments. ", - "Please specify the 'type' argument.") - } - if (nrow(dataset) == 0) { - stop("Could not find data set for station with mode = \"", mode, "\" ", - "and resource_id = \"", resource_id, "\" and type = \"", type, "\"", sep = "") - } else if (nrow(dataset) > 1) { - stop("Multiple matches; should not happen!") + # More than one match? + if (nrow(dataset) > 1L && is.null(type)) { + stop("Found ", nrow(dataset), " datasets matching the input arguments. ", + "Please specify the 'type' argument.") + } + if (nrow(dataset) == 0) { + stop("Could not find data set for station with mode = \"", mode, "\" ", + "and resource_id = \"", resource_id, "\" and type = \"", type, "\"", sep = "") + } else if (nrow(dataset) > 1) { + stop("Multiple matches; should not happen!") + } + dataset <- as.list(dataset) + } else { + # Ensure mode/resource_id are characters of length 1 + stopifnot("argument `mode` must be character length 1" = + is.character(mode) && length(mode) == 1) + stopifnot("argument `resource_id` must be character length 1" = + is.character(resource_id) && length(resource_id) == 1) + # Guess + dataset <- list(url = paste(gs_baseurl(version), "station", mode, resource_id, sep = "/")) } - dataset <- as.list(dataset) - - # Downloading meta data - URL <- paste(dataset$url, "metadata", sep = "/") # Verbosity if (verbose) message("Requesting data for mode = \"", mode, - "\" and resource_id = \"", resource_id, "\"\nCalling: ", URL, sep = "") + "\" and resource_id = \"", resource_id, "\"", sep = "") - # Performing request - req <- GET(URL, config = config) - if (!status_code(req) == 200) { - tmp <- try(content(req)) - if (is.list(tmp) && !is.null(tmp$detail[[1]]$msg)) { - stop(tmp$detail[[1]]$msg) - } else { - stop("HTTP request error: got status code", status_code(req)) - } - } - res <- content(req) - if (inherits(res, "xml_document")) - stop("HTTP request returned HTML; data set requires login (todo)") - res$url <- URL # appending API endpoint URL + # Downloading meta data + res <- API_GET(paste(dataset$url, "metadata", sep = "/"), + config = config, query = NULL, verbose = verbose) # Evaluate result res$parameters <- do.call(rbind, lapply(res$parameters, as.data.frame)) - res$stations <- do.call(rbind, lapply(res$stations, function(x) as.data.frame(lapply(x, function(x) ifelse(is.null(x), NA, x))))) + res$stations <- do.call(rbind, lapply(res$stations, + function(x) as.data.frame(lapply(x, function(x) ifelse(is.null(x), NA, x))))) # Double-check if my format specification below is OK stopifnot("unexpected time format" = all(grepl("\\+00:00$", res$stations$valid_from))) @@ -121,6 +128,6 @@ gs_metadata <- function(mode, resource_id, type = NULL, version = 1L, config = l # Convert to sf data.frame res$stations <- st_as_sf(res$stations, coords = c("lon", "lat"), crs = 4326) - return(res) + return(res) } diff --git a/R/station.R b/R/station.R index 9b998ea..53fa1fd 100644 --- a/R/station.R +++ b/R/station.R @@ -15,7 +15,7 @@ #' @param expert logical, defaults to \code{FALSE}. If \code{TRUE} the script will not #' check if the input arguments are valid. May result in unsuccessful requests #' but increases the speed as \code{gs_datasets()} and \code{gs_metadata()} -#' do not have to be evaluated. +#' do not have to be called (two API requests less). #' @param version integer, API version (defaults to \code{1L}). #' @param drop logical, if \code{TRUE} parameters and times with no data are removed #' before returning the data. @@ -28,9 +28,9 @@ #' @param config empty list by default; can be a named list to be fowrarded #' to the \code{httr::GET} request if needed. #' -#' @details This function is a convenience function for downloading different sets of -#' station data from the GeoSphere Austria data hub (formerly ZAMG). The API may change and additional -#' resources may be added, for details see +#' @details This function is a convenience function for downloading different +#' sets of station data from the GeoSphere Austria data hub (formerly ZAMG). +#' The API may change and additional resources may be added, for details see #' . #' #' To see what's available call \code{gs_datasets("station")}. @@ -39,9 +39,6 @@ #' is based on the number of expecte elements (i.e., number of stations times number #' of parameters times number of time steps). This function will pre-calculate the number #' of expected elements and split the request into batches along the time dimension - if needed. -#' For current limits see -#' . -#' #' @return If only data for one single station (\code{length(station_ids) == 1}) is requested, #' a \code{zoo} object will be returned if data is available. If no data is available, #' \code{NULL} will be returned. @@ -179,20 +176,21 @@ #' @importFrom utils head tail #' @importFrom sf st_point #' @importFrom parsedate parse_iso_8601 -#' @importFrom httr GET status_code content -#' @importFrom zoo zoo index +#' @importFrom zoo zoo index coredata gs_stationdata <- function(mode, resource_id, parameters = NULL, start = NULL, end = NULL, station_ids, expert = FALSE, version = 1L, drop = TRUE, verbose = FALSE, format = NULL, limit = 2e5, config = list()) { - stopifnot("argument 'mode' must be character of length 1" = is.character(mode) & length(mode) == 1L) - stopifnot("argument 'resource_id' must be character of length 1" = is.character(resource_id) & length(resource_id) == 1L) + stopifnot("argument 'mode' must be character of length 1" = + is.character(mode) & length(mode) == 1L) + stopifnot("argument 'resource_id' must be character of length 1" = + is.character(resource_id) & length(resource_id) == 1L) stopifnot("argument 'parameters' must be NULL or a character vector of length > 0" = is.null(parameters) || (is.character(parameters) & length(parameters) > 0)) - stopifnot("argument expert must be logical TRUE or FALSE" = isTRUE(expert) || isFALSE(expert)) - stopifnot("argument drop must be logical TRUE or FALSE" = isTRUE(drop) || isFALSE(drop)) + stopifnot("argument expert must be logical TRUE or FALSE" = isTRUE(expert) || isFALSE(expert)) + stopifnot("argument drop must be logical TRUE or FALSE" = isTRUE(drop) || isFALSE(drop)) stopifnot("argument verbose must be logical TRUE or FALSE" = isTRUE(verbose) || isFALSE(verbose)) # Matching 'mode'. @@ -325,15 +323,8 @@ gs_stationdata <- function(mode, resource_id, parameters = NULL, start = NULL, tmp <- paste(names(tmp), unname(tmp), sep = "=", collapse = "&") message("Calling: ", dataset$url, "?", tmp, sep = "") } - req <- GET(dataset$url, query = query, config = config) - content <- content(req) - if (!status_code(req) == 200) { - if (is.list(content) && "message" %in% names(content) && grepl("timing out", content$message)) { - stop("Request most likely too big. Server responded with: ", content$message) - } else { - stop(content, "\nData request not successful (status code != 200)") - } - } + # Downloading meta data + content <- API_GET(dataset$url, config = config, query = query, verbose = verbose) # Extracting data (lists) final <- list() # To store data @@ -363,7 +354,6 @@ gs_stationdata <- function(mode, resource_id, parameters = NULL, start = NULL, observations = observations)) } # Function for combining the data - ####comb <- function(s) do.call(rbind, lapply(data, function(x, s) x[[s]], s = s)) data <- lapply(batches, get_batch) # Remove overlapping indices as sometimes returned by the API diff --git a/inst/tinytest/test_00_helper.R b/inst/tinytest/test_00_helper.R index 1b3770d..bab0090 100644 --- a/inst/tinytest/test_00_helper.R +++ b/inst/tinytest/test_00_helper.R @@ -4,6 +4,9 @@ if (interactive()) library("tinytest") +# ------------------------------------------------------- +# Temporal interval 'decoder' +# ------------------------------------------------------- # Testing extrating temporal interval from resource ID expect_error(gs_temporal_interval()) expect_error(gs_temporal_interval(3)) @@ -33,3 +36,36 @@ expect_silent(t <- gs_temporal_interval(tmp), info = "Checking correct usage.") expect_identical(t, rep(c(366L * 86400L, 31L * 86400L), 2), info = "Checking for correct return and correct calculation (3/3)") + + +# ------------------------------------------------------- +# Show http status and terminate +# ------------------------------------------------------- +expect_error(gsdata:::show_http_status_and_terminate(), + info = "Testing usage - no input") +expect_error(gsdata:::show_http_status_and_terminate(1:2), + info = "Testing usage - wrong input") +expect_error(gsdata:::show_http_status_and_terminate("foo"), + info = "Testing usage - wrong input") +expect_silent(gsdata:::show_http_status_and_terminate(200), + info = "Testing behaviour if status code is in range 200") +expect_silent(gsdata:::show_http_status_and_terminate(201), + info = "Testing behaviour if status code is in range 200") +expect_identical(gsdata:::show_http_status_and_terminate(200), NULL, + info = "Return NULL if status code is in the 200 range") + +expect_error(gsdata:::show_http_status_and_terminate(400), + pattern = ".*Client error.*Bad Request.*", + info = "Testing error message for status code 400; no xtra") +expect_error(gsdata:::show_http_status_and_terminate(400), + pattern = "http_status description.*Client error.*Bad Request.*", + info = "Testing error message for status code 400; no xtra") +expect_error(gsdata:::show_http_status_and_terminate(400, list(xtra = "custom error")), + pattern = "HTTP request error.*status returned by API.*xtra:.*custom error.*Client error.*Bad Request.*", + info = "Testing error message for status code 400; with xtra") +expect_error(gsdata:::show_http_status_and_terminate(99999), + pattern = "HTTP request error: server returned status code 99999", + info = "Testing status code not recognized by http_status.") + + + diff --git a/inst/tinytest/test_01_gs_datasets.R b/inst/tinytest/test_01_gs_datasets.R index bfd2c4d..d3ef49d 100644 --- a/inst/tinytest/test_01_gs_datasets.R +++ b/inst/tinytest/test_01_gs_datasets.R @@ -4,6 +4,8 @@ if (interactive()) library("tinytest") +options("gsdata.cooldown" = 0.5) + expect_silent(ds <- gs_datasets(), info = "Calling dataset endpoint") expect_inherits(ds, "data.frame", diff --git a/inst/tinytest/test_03_stationdata.R b/inst/tinytest/test_03_stationdata.R index 3ca6695..d513cf5 100644 --- a/inst/tinytest/test_03_stationdata.R +++ b/inst/tinytest/test_03_stationdata.R @@ -4,6 +4,8 @@ if (interactive()) library("tinytest") +options("gsdata.cooldown" = 0.5) + # Misuse expect_error(do.call(gs_stationdata, tmp), info = "Stations do not exist") diff --git a/man/API_GET.Rd b/man/API_GET.Rd new file mode 100644 index 0000000..463e6ac --- /dev/null +++ b/man/API_GET.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/helperfunctions.R +\name{API_GET} +\alias{API_GET} +\title{Handling API Calls} +\usage{ +API_GET( + URL, + config = NULL, + query = NULL, + expected_class = NULL, + verbose = FALSE +) +} +\arguments{ +\item{URL}{the URL to be called.} + +\item{config}{\code{NULL} or \code{list}, forwarded to \code{httr::GET}.} + +\item{query}{\code{NULL} or \code{list}, forwarded to \code{httr::GET}.} + +\item{expected_class}{\code{NULL} or character vector. If set, it is checked +if the returned object is of this class. If not, a warning will be thrown +(no error).} + +\item{verbose}{logical, shows some additional information if \code{TRUE}.} +} +\value{ +Returns the object we get from \code{httr::content()} after a successful +API call. If an error is detected, an error with additional details will be displayed. +} +\description{ +Small helper function to handle http requests to the API. +} +\author{ +Reto Stauffer +} diff --git a/man/gs_metadata.Rd b/man/gs_metadata.Rd index df9229c..5e5e9cf 100644 --- a/man/gs_metadata.Rd +++ b/man/gs_metadata.Rd @@ -10,6 +10,7 @@ gs_metadata( type = NULL, version = 1L, config = list(), + expert = FALSE, verbose = FALSE ) } @@ -26,6 +27,11 @@ is available in more than one type (e.g., \"grid\" and \"timeseries\").} \item{config}{empty list by default; can be a named list to be fowrarded to the \code{httr::GET} request if needed.} +\item{expert}{logical, defaults to \code{FALSE}. If \code{TRUE} the script will not +check if the input arguments are valid. May result in unsuccessful requests +but increases the speed as \code{gs_datasets()} does not have to be +called (one less API request).} + \item{verbose}{logical, if set \code{TRUE} some more output will be produced.} } \value{ diff --git a/man/gs_stationdata.Rd b/man/gs_stationdata.Rd index 68be04f..8ef0955 100644 --- a/man/gs_stationdata.Rd +++ b/man/gs_stationdata.Rd @@ -36,7 +36,7 @@ Not needed (ignored) when \code{mode = "current"}.} \item{expert}{logical, defaults to \code{FALSE}. If \code{TRUE} the script will not check if the input arguments are valid. May result in unsuccessful requests but increases the speed as \code{gs_datasets()} and \code{gs_metadata()} -do not have to be evaluated.} +do not have to be called (two API requests less).} \item{version}{integer, API version (defaults to \code{1L}).} @@ -68,9 +68,9 @@ Accessing the API endpoint \code{v/station}, see \url{https://dataset.api.hub.geosphere.at/v1/docs/getting-started.html}. } \details{ -This function is a convenience function for downloading different sets of -station data from the GeoSphere Austria data hub (formerly ZAMG). The API may change and additional -resources may be added, for details see +This function is a convenience function for downloading different +sets of station data from the GeoSphere Austria data hub (formerly ZAMG). +The API may change and additional resources may be added, for details see \url{https://dataset.api.hub.geosphere.at/v1/docs/user-guide/endpoints.html}. To see what's available call \code{gs_datasets("station")}. @@ -79,8 +79,6 @@ The API has a limit for the number of elements for one request. The calculation is based on the number of expecte elements (i.e., number of stations times number of parameters times number of time steps). This function will pre-calculate the number of expected elements and split the request into batches along the time dimension - if needed. -For current limits see -\url{https://dataset.api.hub.geosphere.at/v1/docs/user-guide/request_size_limit.html}. } \examples{ ###################################################################### diff --git a/man/gsdata.Rd b/man/gsdata.Rd new file mode 100644 index 0000000..465b509 --- /dev/null +++ b/man/gsdata.Rd @@ -0,0 +1,74 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/gsdata.R +\docType{package} +\name{gsdata} +\alias{gsdata} +\alias{gsdata-package} +\title{\code{gsdata}: Interface to the GeoSphere Austria DataHub API (Data Access)} +\description{ +This package allows convenient access to data provided by GeoSphere Austria +(Austrias federal agency for geology, geophysics, climatology and +meteorology) via their data API which exists since around mid 2023. +} +\details{ +The API not only provides access to station data (the one thing currently +covered by this package; will be extended) but also access to spatial +data; a catalogue which has been extended over and over again over the past +10 months. Details about all available data sets and their temporal and +spatial extent can be found on their website: + +\itemize{ +\item \url{https://data.hub.geosphere.at/} +} +} +\section{Data request limit}{ + + +The API has a request limit; a limit to how much data one is allowed +to retrieve in one API request. Details on the current limit can be found +in the \href{https://dataset.api.hub.geosphere.at/v1/docs/user-guide/request_size_limit.html}{GeoSphere Dataset API Documentation}. + +This package internally tries to estimate the request size and split the +request into multiple batches in case one single request would (likely) +exceed these limits. + +Thus, one single call to e.g., \code{gs_stationdata()} can trigger multiple +API calls. If used without \code{expert = TRUE} two initial calls are made to +check if the data set requested does exist, and that the +stations and parameters requested exist in this data set. If the data request +needs to be split in addition, this can cause a series of calls to the API +which also has a limit on number of requests per time. + +In the worst case this causes a temporary ban (timeout due to too many requests) +from the servers. One way around is to limit the number of requests per time, +more details about this in the next section. +} + +\section{Cooldown time/limiting number of requests per time}{ + + +Note that each function call can result in multiple API requests which can +lead to a timeout (too many requests). To avoid running into timeout issues: + +\itemize{ +\item use \code{expert = TURUE} where possible as it +lowers the number of calls to the api. +\item request data for multiple stations at once, especially +when requesting short time periods/few parameters as, in the best case, +all data can be retrieved on one single call (if below estimated +data request limit). +\item wait between requests using e.g., \code{Sys.sleep(...)}. +\item or use the packages own 'cooldown' option. By default, +a cooldown time of \code{0.1} seconds is used (the minimum +time between two requests. You can set a custom cooldown time +via \code{options('gsdata.cooldown' = 1)}. Will overwrite the +default and ensure that there will be at least one second +between consecutive API calls. If you have no time critical +requests this is a good way to be nice to the data provider! +} +} + +\author{ +\strong{Maintainer}: Reto Stauffer \email{reto.stauffer@uibk.ac.at} (\href{https://orcid.org/0000-0002-3798-5507}{ORCID}) + +} diff --git a/man/show_http_status_and_terminate.Rd b/man/show_http_status_and_terminate.Rd new file mode 100644 index 0000000..afa066e --- /dev/null +++ b/man/show_http_status_and_terminate.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/helperfunctions.R +\name{show_http_status_and_terminate} +\alias{show_http_status_and_terminate} +\title{Show HTTP Error Status and Terminate} +\usage{ +show_http_status_and_terminate(scode, xtra = NULL) +} +\arguments{ +\item{scode}{numeric, http status code.} + +\item{xtra}{\code{NULL} or named list with additional information.} +} +\value{ +No return, will terminate R. +} +\description{ +This function is called whenever \code{httr::GET} returns an +http status code out of the \code{200} range (success). +Shows \code{\link[http]{http_status()}} code information alongside +with additional messages returned by the API (if any). +} +\author{ +Reto Stauffer +} diff --git a/tests/tinytest.R b/tests/tinytest.R index cb98a0e..ede3a29 100644 --- a/tests/tinytest.R +++ b/tests/tinytest.R @@ -1,6 +1,5 @@ if (requireNamespace("tinytest", quietly = TRUE)) { - require("tinytest") - test_package("gsdata") + tinytest::test_package("gsdata") } diff --git a/vignettes/datasets.Rmd b/vignettes/datasets.Rmd index 875e0d3..6c2f3d8 100644 --- a/vignettes/datasets.Rmd +++ b/vignettes/datasets.Rmd @@ -8,11 +8,11 @@ output: theme: flatly link-citations: true vignette: > - %\VignetteIndexEntry{annex: Annex86 Data Analysis Package} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteDepends{Formula} - %\VignetteKeywords{Annex86} - %\VignettePackage{annex} + %\VignetteIndexEntry{gsdata: Datasets} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteDepends{gsdata} + %\VignetteKeywords{GeoSphere, datasets} + %\VignettePackage{gsdata} --- ```{r, include = FALSE} @@ -23,6 +23,10 @@ Returns available data sets. Note that the current default is set to `type = "station"` (see `gs_datasets()`) as this package only allows for downloading stationdata. +```{r, include = FALSE} +options("gsdata.cooldown" = 1) +``` + ```{r} library("gsdata") (ds <- gs_datasets()) diff --git a/vignettes/metadata.Rmd b/vignettes/metadata.Rmd index 53a55fa..27d6580 100644 --- a/vignettes/metadata.Rmd +++ b/vignettes/metadata.Rmd @@ -1,5 +1,5 @@ --- -title: "Datasets" +title: "Metadata" author: "Reto Stauffer" output: html_document: @@ -8,15 +8,16 @@ output: theme: flatly link-citations: true vignette: > - %\VignetteIndexEntry{annex: Annex86 Data Analysis Package} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteDepends{Formula} - %\VignetteKeywords{Annex86} - %\VignettePackage{annex} + %\VignetteIndexEntry{gsdata: Metadata} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteDepends{gsdata} + %\VignetteKeywords{GeoSphere, meta data} + %\VignettePackage{gsdata} --- ```{r, include = FALSE} library("gsdata") +options("gsdata.cooldown" = 1) ``` Given `mode` and the `resource_id` are known (see `gs_datasets()`) diff --git a/vignettes/overview.Rmd b/vignettes/overview.Rmd new file mode 100644 index 0000000..f42357b --- /dev/null +++ b/vignettes/overview.Rmd @@ -0,0 +1,49 @@ +--- +title: "Datasets" +author: "Reto Stauffer" +output: + rmarkdown::html_vignette: + highlight: monochrome + toc: true +link-citations: true +vignette: > + %\VignetteIndexEntry{Package Overview} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteDepends{gsdata} + %\VignetteKeywords{GeoSphere, datasets} + %\VignettePackage{gsdata} +--- + +```{r, include = FALSE} +library("gsdata") +``` + +TODO(R): Ovrview vignett for R CMD build; the only vignette we'll +include (rest is pkgdown content). + +Returns available data sets. Note that the current default is set to +`type = "station"` (see `gs_datasets()`) as this package only allows +for downloading stationdata. + +```{r, include = FALSE} +options("gsdata.cooldown" = 1) +``` + +```{r} +library("gsdata") +(ds <- gs_datasets()) +``` + +The function `gs_datasets()` returns a `data.frame` which includes +a series of information including: + +* `type`: data set type (currently defaults to `type = "station"`) +* `mode`: historical or current (latest available observation) +* `resource_id`: ID/name of the dataset or resource +* ... and some more + +Most important are `type`, `mode` and `resource_id` which allow +to download additional meta data (see `gs_metadata()`) as well +as the data itself (see `gs_stationdata()`). + + diff --git a/vignettes/stationdata.Rmd b/vignettes/stationdata.Rmd index ba6a994..f77c03f 100644 --- a/vignettes/stationdata.Rmd +++ b/vignettes/stationdata.Rmd @@ -1,5 +1,5 @@ --- -title: "Datasets" +title: "Stationdata" author: "Reto Stauffer" output: html_document: @@ -8,16 +8,17 @@ output: theme: flatly link-citations: true vignette: > - %\VignetteIndexEntry{annex: Annex86 Data Analysis Package} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteDepends{Formula} - %\VignetteKeywords{Annex86} - %\VignettePackage{annex} + %\VignetteIndexEntry{gsdata: Station Data} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteDepends{gsdata} + %\VignetteKeywords{GeoSphere, station data} + %\VignettePackage{gsdata} --- ```{r setup, include = FALSE} suppressPackageStartupMessages(library('zoo')) library("gsdata") +options("gsdata.cooldown" = 1) ``` This article contains a series of examples on how to retrieve @@ -72,7 +73,6 @@ do not exist. One can, of course, get the meta information for the station and parameters if needed (see `gs_metdatata()` for more details): - ```{r meta_hist_synop} meta <- gs_metadata(mode = "historical", resource_id = "synop-v1-1h") subset(meta$stations, id == 11330)