first commit

.Rbuildignore

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+^\.travis\.yml$
+^.*\.Rproj$
+^.*\.Renviron$
+^\.Rproj\.user$
+^README\.Rmd$
+^README\.md$
+^_config\.yml$
+^cran-comments\.md$
+^CONDUCT\.md$
+^NEWS\.md$
+^LICENSE$

.gitignore

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+.Rproj.user
+.Rhistory
+.Renviron
+.RData
+.Ruserdata
+inst/doc

.travis.yml

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+language: R
+sudo: required
+cache: packages
+warnings_are_errors: true
+
+before_install:
+  - sudo apt-get install --yes udunits-bin libudunits2-dev
+  - sudo apt-get install --yes libproj-dev libgeos-dev libgdal-dev libgdal1-dev
+  - sudo apt-get install --yes libnetcdf-dev netcdf-bin
+
+r:
+  - release
+  - devel
+
+r_packages:
+  - devtools
+  - covr
+
+after_success:
+  - Rscript -e 'covr::codecov()'

CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant 
+(http:contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

DESCRIPTION

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+Package: ecmwfr
+Title: Interface to the public 'ECMWF' Web Services
+Version: 0.0.2
+Authors@R: person("Hufkens","Koen",
+		  email="[email protected]",
+		  role=c("aut", "cre"))
+Description: Programmatic interface to the 'ECMWF' public dataset 
+    web services. Allows for easy downloads of
+    climate data directly to your R workspace or your computer.
+Depends:
+    R (>= 3.4.0)
+Imports:
+    httr,
+    keyring
+License: AGPL-3
+LazyData: true
+ByteCompile: true
+RoxygenNote: 6.1.0
+Suggests:
+    knitr,
+    rmarkdown,
+    covr,
+    testthat
+VignetteBuilder: knitr

NEWS.md

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+# ecmwfr 0.0.2
+
+* working verion, yeah!
+
+
+# ecmwfr 0.0.1
+
+* experimental release
+* trying to get things working

R/ecmwf_delete.R

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+#' ECMWF delete request
+#'
+#' Deletes a staged download from the queue
+#'
+#' @param email email address used to sign up for the ECMWF data service and
+#' used to retrieve the token set by \code{\link[ecmwfr]{ecmwf_set_key}}
+#' @param url url to query
+#' @keywords data download, climate, re-analysis
+#' @seealso \code{\link[ecmwfr]{ecmwf_set_key}}
+#' \code{\link[ecmwfr]{ecmwf_download}}
+#' \code{\link[ecmwfr]{ecmwf_request}}
+#' @export
+#' @examples
+#'
+#' \donttest{
+#' # set key
+#' ecmwf_set_key(email = "[email protected]", key = "123")
+#'
+#' # get key
+#' ecmwf_get_key(email = "[email protected]")
+#'}
+
+
+ecmwf_delete <- function(
+  email,
+  url
+){
+
+  # check the login credentials
+  if(missing(email) | missing(url)){
+    stop("Please provide ECMWF login email / url!")
+  }
+
+  # get key from email
+  key <- ecmwf_get_key(email)
+
+  # Finally when all went well we have to remove the subset
+  # from the queued list so that memory is de-allocated on the
+  # ECMWF server!
+  response <- httr::DELETE(
+    url,
+    httr::add_headers(
+      "Accept" = "application/json",
+      "Content-Type" = "application/json",
+      "From" = email,
+      "X-ECMWF-KEY" = key)
+  )
+
+  # check purging of request
+  if(response$status == 204){
+    message("Request purged from queue!")
+  } else {
+    warning("Request not purged from queue, check download!")
+  }
+}

R/ecmwf_download.R

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+#' ECMWF download request
+#'
+#' Returns the contents of the requested url as a netCDF file downloaded
+#' to disk.
+#'
+#' @param email email address used to sign up for the ECMWF data service and
+#' used to retrieve the token set by \code{\link[ecmwfr]{ecmwf_set_key}}
+#' @param url url to query
+#' @param path path were to store the downloaded data
+#' @param filename filename to use for the downloaded data
+#' @return a netCDF of data on disk as specified by a
+#' \code{\link[ecmwfr]{ecmwf_request}}
+#' @keywords data download, climate, re-analysis
+#' @seealso \code{\link[ecmwfr]{ecmwf_set_key}}
+#' \code{\link[ecmwfr]{ecmwf_download}}
+#' \code{\link[ecmwfr]{ecmwf_request}}
+#' @export
+#' @examples
+#'
+#' \donttest{
+#' # set key
+#' ecmwf_set_key(email = "[email protected]", key = "123")
+#'
+#' # get key
+#' ecmwf_get_key(email = "[email protected]")
+#'}
+
+
+ecmwf_download <- function(
+  email,
+  url,
+  path = tempdir(),
+  filename = "ecmwf_tmp.nc"
+){
+
+  # check the login credentials
+  if(missing(email) | missing(url)){
+    stop("Please provide ECMWF login email / url!")
+  }
+
+  # get key from email
+  key <- ecmwf_get_key(email)
+
+  # create temporary output file
+  ecmwf_tmp_files <- file.path(tempdir(), filename)
+
+  # provide some feedback on the url which is
+  # downloaded
+  message("Downloading request at:")
+  message(ct$href)
+
+  # submit download query
+  response <- httr::GET(
+    ct$href,
+    httr::add_headers(
+      "Accept" = "application/json",
+      "Content-Type" = "application/json",
+      "From" = email,
+      "X-ECMWF-KEY" = key),
+    httr::progress(),
+    encode = "json",
+    httr::write_disk(path = ecmwf_tmp_file, overwrite = TRUE)
+  )
+
+  # trap errors on download, return a general error statement
+  if (httr::http_error(response)){
+    stop("Your requested download failed", call. = FALSE)
+  }
+}

R/ecmwf_get_key.R

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+#' Get secret ECMWF token
+#'
+#' Returns you token set by ecmwf_set_key()
+#'
+#' @param email email address used to sign up for the ECMWF data service
+#' @return the key set using ecmwf_set_key() saved in the keychain
+#' @keywords key management
+#' @seealso \code{\link[ecmwfr]{ecmwf_set_key}}
+#' @export
+#' @examples
+#'
+#' \donttest{
+#' # set key
+#' ecmwf_set_key(email = "[email protected]", key = "123")
+#'
+#' # get key
+#' ecmwf_get_key(email = "[email protected]")
+#'}
+
+ecmwf_get_key <- function(email, key){
+  keyring::key_get(service = "ecmwfr",
+                   username = email)
+}

R/ecmwf_request.R

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+#' ECMWF data request and download
+#'
+#' Stage a data request, and optionally download the data to disk. Alternatively
+#' you can only stage requests, logging the request URLs to submit download
+#' queries later on using \code{\link[ecmwfr]{ecmwf_download}}
+#'
+#' @param email email address used to sign up for the ECMWF data service and
+#' used to retrieve the token set by \code{\link[ecmwfr]{ecmwf_set_key}}
+#' @param path path were to store the downloaded data
+#' @param time_out how long to wait on a download to start
+#' @param download logical, download data TRUE or FALSE (default = FALSE)
+#' @param request nested list with query parameters following the layout
+#' as specified on the ECMWF API page
+#' @return a download query staging url or a netCDF of data on disk
+#' @keywords data download, climate, re-analysis
+#' @seealso \code{\link[ecmwfr]{ecmwf_set_key}}
+#' \code{\link[ecmwfr]{ecmwf_download}}
+#' \code{\link[ecmwfr]{ecmwf_status}}
+#' @export
+#' @examples
+#'
+#' \donttest{
+#' # set key
+#' ecmwf_set_key(email = "[email protected]", key = "123")
+#'
+#' # get key
+#' ecmwf_get_key(email = "[email protected]")
+#'}
+
+ecmwf_request <- function(
+  email,
+  path = tempdir(),
+  time_out = 3600,
+  download = FALSE,
+  request = list(stream = "oper",
+                 levtype = "sfc",
+                 param = "165.128/166.128/167.128",
+                 dataset = "interim",
+                 step = "0",
+                 grid = "0.75/0.75",
+                 time = "00/06/12/18",
+                 date = "2014-07-01/to/2014-07-31",
+                 type = "an",
+                 class = "ei",
+                 area = "73.5/-27/33/45",
+                 format = "netcdf",
+                 target = "tmp.nc")){
+
+  # check the login credentials
+  if(missing(email) | missing(request)){
+    stop("Please provide ECMWF login credentials and data request!")
+  }
+
+  # get key from email
+  key <- ecmwf_get_key(email)
+
+  # get the response from the query provided
+  response <- httr::POST(
+    paste(ecmwf_server(),
+          "datasets",
+          request$dataset,
+          "requests", sep = "/"),
+    httr::add_headers(
+      "Accept" = "application/json",
+      "Content-Type" = "application/json",
+      "From" = email,
+      "X-ECMWF-KEY" = key),
+    body = request,
+    encode = "json"
+    )
+
+  # line to trap general httr error (server not reachable etc.)
+
+  # grab content, to look at the status
+  ct <- httr::content(response)
+
+  # if the status code is >= 400 stop
+  if(ct$code >= 400){
+    stop("Your request was malformed, check your request statement",
+         call. = FALSE)
+  }
+
+  # only return the content of the query
+  if(!download){
+    return(ct)
+  }
+
+  # set spinner count for some feedback
+  # downloads can take a while it seems
+  spinner_count <- 1
+
+  # start time-out counter
+  time_out_start <- Sys.time()
+
+  # keep waiting for the download order to come online
+  # with status code 303
+  while(ct$code == 202){
+
+    # update spinner count
+    spinner_count <- ifelse(spinner_count < 4, spinner_count + 1, 1)
+
+    # update spinner message
+    message(paste0(c("-","\\","|","/")[spinner_count],
+                   " Your request is ",
+                   ct$status,
+                   ", waiting on server response...\r"), appendLF = FALSE)
+
+    # sleep for the time (in seconds) provided
+    # in the content returned upon query
+    Sys.sleep(ct$retry)
+
+    # check the status of the download, no download
+    ct <- ecmwf_status(email = email, url = ct$href)
+  }
+
+  # if the http code is 303 (a redirect)
+  # follow this query and download the data
+  if(ct$code == 303){
+    ecmwf_download(email = email)
+  }
+
+  # Copy data from temporary file to final location
+  # and delete original, with an exception for tempdir() location.
+  # The latter to facilitate package integration.
+  if (path != tempdir()) {
+
+    # copy temporary file to final destination
+    file.copy(ecmwf_tmp_file,
+              file.path(path, request$target),
+              overwrite = TRUE,
+              copy.mode = FALSE)
+
+    # cleanup of temporary file
+    invisible(file.remove(ecmwf_tmp_file))
+  } else {
+    message("Output path == tempdir(), file not copied and removed!")
+  }
+
+  # delete the request upon succesful download
+  ecmwf_delete(email = email, url = ct$href)
+}