update from main

CITATION.cff

@@ -8,7 +8,8 @@ message: 'To cite package "getRad" in publications use:'
 type: software
 license: MIT
 title: 'getRad: Download Radar Data for Biological Research'
-version: 0.2.0
+version: 0.2.0.9000
+doi: 10.32614/CRAN.package.getRad
 abstract: Load polar volume and vertical profile data for aeroecological research
   directly into R. With 'getRad' you can access data from several sources in Europe
   and the US and standardize it to facilitate further exploration in tools such as
@@ -29,6 +30,7 @@ authors:
   email: peter.desmet@inbo.be
   orcid: https://orcid.org/0000-0002-8442-8025
   affiliation: Research Institute for Nature and Forest (INBO)
+repository: https://CRAN.R-project.org/package=getRad
 repository-code: https://github.com/aloftdata/getRad
 url: https://aloftdata.github.io/getRad/
 contact:
@@ -267,6 +269,31 @@ references:
     orcid: https://orcid.org/0000-0002-6983-2759
   year: '2025'
   doi: 10.32614/CRAN.package.vroom
+- type: software
+  title: withr
+  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
+  notes: Imports
+  url: https://withr.r-lib.org
+  repository: https://CRAN.R-project.org/package=withr
+  authors:
+  - family-names: Hester
+    given-names: Jim
+  - family-names: Henry
+    given-names: Lionel
+    email: lionel@posit.co
+  - family-names: Müller
+    given-names: Kirill
+    email: krlmlr+r@mailbox.org
+  - family-names: Ushey
+    given-names: Kevin
+    email: kevinushey@gmail.com
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+  - family-names: Chang
+    given-names: Winston
+  year: '2025'
+  doi: 10.32614/CRAN.package.withr
 - type: software
   title: xml2
   abstract: 'xml2: Parse XML'
@@ -483,29 +510,4 @@ references:
     orcid: https://orcid.org/0000-0001-6573-066X
   year: '2025'
   doi: 10.32614/CRAN.package.vol2birdR
-- type: software
-  title: withr
-  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
-  notes: Suggests
-  url: https://withr.r-lib.org
-  repository: https://CRAN.R-project.org/package=withr
-  authors:
-  - family-names: Hester
-    given-names: Jim
-  - family-names: Henry
-    given-names: Lionel
-    email: lionel@posit.co
-  - family-names: Müller
-    given-names: Kirill
-    email: krlmlr+r@mailbox.org
-  - family-names: Ushey
-    given-names: Kevin
-    email: kevinushey@gmail.com
-  - family-names: Wickham
-    given-names: Hadley
-    email: hadley@posit.co
-  - family-names: Chang
-    given-names: Winston
-  year: '2025'
-  doi: 10.32614/CRAN.package.withr
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: getRad
 Title: Download Radar Data for Biological Research
-Version: 0.2.0.9000
+Version: 0.2.2.9000
 Authors@R: c(
     person("Bart", "Kranstauber", , "b.kranstauber@uva.nl", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8303-780X", affiliation = "University of Amsterdam")),
@@ -15,7 +15,7 @@ Authors@R: c(
     person("Hidde", "Leijnse", role = "ctb",
            comment = c(ORCID = "0000-0001-7835-4480", affiliation = "Royal Netherlands Meteorological Institute")),
     person("Bart", "Hoekstra", role = "ctb",
-           comment = c(ORCID = " 0000-0002-7085-3805", affiliation = "University of Amsterdam")),
+           comment = c(ORCID = "0000-0002-7085-3805", affiliation = "University of Amsterdam")),
     person("University of Amsterdam", role = "cph",
            comment = c(ROR = "04dkp9463")),
     person("Biodiversa+", role = "fnd",
@@ -45,6 +45,7 @@ Imports:
     tools,
     utils,
     vroom,
+    withr,
     xml2
 Suggests:
     askpass,
@@ -58,8 +59,7 @@ Suggests:
     sf,
     testthat (>= 3.0.0),
     tidyr,
-    vol2birdR,
-    withr
+    vol2birdR
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3

NEWS.md

@@ -1,7 +1,20 @@
 # getRad (development version)
 
-* Support downloading Swedish data (#96).
+# getRad 0.2.2
+
+* Support downloading Slovakian polar volume data (#124).
+* Add retry attempts to `get_weather_radars` for NEXRAD to prevent failure (#116).
+* Update of NEXRAD url (#118).
+* Fix CRAN warning where cache was not cleaned after tests (#122).
+* Resolve `withr` error for Danish radars.
+
+# getRad 0.2.1
+
+* A bug (#101) in `get_vpts()` was fixed that caused the function to only return the first day of an interval, regardless of the length of the interval (#105).
+* Support downloading Swedish polar volume data (#96).
+* Support downloading Romanian polar volume data (#104).
 * How attribute is now present in Czech data (#102).
+* Use `withr` to prevent files being left in temporary directories (#98).
 
 # getRad 0.2.0
 

R/get_pvol.R

@@ -120,6 +120,7 @@ get_pvol <- function(radar = NULL, datetime = NULL, ...) {
 
 
 # Helper function to find the function for a specific radar
+# This function is only helpful in get_pvol and therefor not in a utils file
 select_get_pvol_function <- function(radar, ..., call = rlang::caller_env()) {
   if (is_nexrad(radar)) {
     return("get_pvol_us")
@@ -133,6 +134,8 @@ select_get_pvol_function <- function(radar, ..., call = rlang::caller_env()) {
     cntry_code == "ee" ~ "get_pvol_ee",
     cntry_code == "cz" ~ "get_pvol_cz",
     cntry_code == "se" ~ "get_pvol_se",
+    cntry_code == "ro" ~ "get_pvol_ro",
+    cntry_code == "sk" ~ "get_pvol_sk",
     .default = NA
   ))
   if (rlang::is_na(fun)) {
@@ -144,3 +147,5 @@ select_get_pvol_function <- function(radar, ..., call = rlang::caller_env()) {
   }
   return(fun)
 }
+
+

R/get_pvol_cz.R

@@ -36,55 +36,6 @@ get_pvol_cz <- function(radar, time, ..., call = rlang::caller_env()) {
         time + lubridate::minutes(5)
       )
     ))
-  files_to_get <- files_to_get |> dplyr::mutate(
-    req = purrr::pmap(list(x = base, y = file), function(x, y) {
-      httr2::request(x) |>
-        httr2::req_url_path_append(y) |>
-        req_user_agent_getrad()
-    })
-  )
-
-
-  files_to_get$resp <- files_to_get$req |>
-    httr2::req_perform_parallel(
-      paths = replicate(
-        length(files_to_get$req),
-        tempfile(fileext = ".h5")
-      )
-    )
-  polar_volumes_tibble <- files_to_get |>
-    dplyr::mutate(
-      tempfile = purrr::map_chr(resp, purrr::chuck, "body"),
-      pvol = purrr::map(tempfile, ~ bioRad::read_pvolfile(.x)),
-      remove = purrr::map(tempfile, ~ file.remove(.x))
-    )
-  # Check if all parameter have same attributes
-  list_of_attribute_tables <- purrr::map(
-    purrr::chuck(polar_volumes_tibble, "pvol"),
-    bioRad::attribute_table
-  )
-  all_params_same_attributes <- all(unlist(lapply(
-    lapply(list_of_attribute_tables[-1], dplyr::select, -"param"), all.equal,
-    dplyr::select(list_of_attribute_tables[[1]], -"param")
-  )))
-  if (!all_params_same_attributes) {
-    cli::cli_abort("Not all polar volumes have the same attributes",
-      class = "getRad_error_differing_attributes_cz", call = call
-    )
-  }
-  pvol <- Reduce(
-    function(x, y) {
-      x$scans <- mapply(
-        function(i, j) {
-          i$params <- c(i$params, j$params)
-          i
-        },
-        x$scans, y$scans,
-        SIMPLIFY = FALSE
-      )
-      x
-    },
-    polar_volumes_tibble$pvol
-  )
+  pvol<-read_pvol_from_url_per_param(paste0(files_to_get$base, files_to_get$file))
   pvol
 }

R/get_pvol_de.R

@@ -59,38 +59,39 @@ get_pvol_de <- function(radar, time, ...,
       }
     )
   )
-
-  files_to_get$resp <- files_to_get$req |>
-    httr2::req_perform_parallel(
-      paths = replicate(
-        length(files_to_get$req),
-        tempfile(fileext = ".h5")
+  pvol <- withr::with_tempdir({
+    files_to_get$resp <- files_to_get$req |>
+      httr2::req_perform_parallel(
+        paths = replicate(
+          length(files_to_get$req),
+          tempfile(fileext = ".h5", tmpdir = getwd())
+        )
       )
+    files_to_get <- files_to_get |>
+      dplyr::mutate(
+        tempfile = purrr::map_chr(resp, ~ .x$body)
+      ) |>
+      dplyr::mutate(
+        scan = purrr::map(tempfile, ~ read_scan(.x)),
+        remove = purrr::map(tempfile, ~ file.remove(.x))
+      ) |>
+      tidyr::separate_wider_delim(sweep,
+        delim = "_", cols_remove = FALSE,
+        names = c("vol", "name", "param", "iter")
+      ) |>
+      dplyr::group_by(iter) |>
+      dplyr::summarize(
+        scan = list(scan),
+        param = list(param), radar = unique(radar)
+      ) |>
+      dplyr::mutate(
+        scan = purrr::map2(scan, param, ~ list_to_scan(.x, .y))
+      )
+    list_to_pvol(files_to_get$scan,
+      time = time, radar = radar,
+      source = glue::glue("NOD:{radar},CMT:constructed from opendata.dwd.de")
     )
-  files_to_get <- files_to_get |>
-    dplyr::mutate(
-      tempfile = purrr::map_chr(resp, ~ .x$body)
-    ) |>
-    dplyr::mutate(
-      scan = purrr::map(tempfile, ~ read_scan(.x)),
-      remove = purrr::map(tempfile, ~ file.remove(.x))
-    ) |>
-    tidyr::separate_wider_delim(sweep,
-      delim = "_", cols_remove = FALSE,
-      names = c("vol", "name", "param", "iter")
-    ) |>
-    dplyr::group_by(iter) |>
-    dplyr::summarize(
-      scan = list(scan),
-      param = list(param), radar = unique(radar)
-    ) |>
-    dplyr::mutate(
-      scan = purrr::map2(scan, param, ~ list_to_scan(.x, .y))
-    )
-  pvol <- list_to_pvol(files_to_get$scan,
-    time = time, radar = radar,
-    source = glue::glue("NOD:{radar},CMT:constructed from opendata.dwd.de")
-  )
+  })
   return(pvol)
 }
 

R/get_pvol_dk.R

@@ -1,20 +1,21 @@
 get_pvol_dk <- function(radar, time, ..., call = rlang::caller_env()) {
-  req <- httr2::request(
-    getOption(
-      "getRad.dk_url",
-      "https://dmigw.govcloud.dk/v1/radardata/download"
-    )
-  ) |>
-    req_user_agent_getrad() |>
-    httr2::req_url_path_append(
-      glue::glue(getOption(
-        "getRad.dk_file_format",
-        "{radar}_{strftime(time,'%Y%m%d%H%M', tz='UTC')}.vol.h5"
-      ))
+ withr::with_file("file.h5", {
+    req <- httr2::request(
+      getOption(
+        "getRad.dk_url",
+        "https://dmigw.govcloud.dk/v1/radardata/download"
+      )
     ) |>
-    httr2::req_url_query(`api-key` = get_secret("dk_api_key")) |>
-    httr2::req_perform(path = tempfile(fileext = ".h5"), error_call = call)
-  pvol <- bioRad::read_pvolfile(req$body, ...)
-  file.remove(req$body)
+      req_user_agent_getrad() |>
+      httr2::req_url_path_append(
+        glue::glue(getOption(
+          "getRad.dk_file_format",
+          "{radar}_{strftime(time,'%Y%m%d%H%M', tz='UTC')}.vol.h5"
+        ))
+      ) |>
+      httr2::req_url_query(`api-key` = get_secret("dk_api_key")) |>
+      httr2::req_perform(path = "file.h5", error_call = call)
+    pvol<-bioRad::read_pvolfile(req$body, ...)
+  })
   return(pvol)
 }

R/get_pvol_ee.R

@@ -25,10 +25,10 @@ get_pvol_ee <- function(radar, time, ...,
         ),
         list(isEqual = list(
           field = "Radar",
-          value = dplyr::case_match(
+          value = radar_recode(
             radar,
-            "eesur" ~ "S\u00FCrgavere radar (SUR)",
-            "eehar" ~ "Harku radar (HAR)"
+            "eesur" = "S\u00FCrgavere radar (SUR)",
+            "eehar" = "Harku radar (HAR)", call = call
           )
         ))
       ))))
@@ -44,13 +44,14 @@ get_pvol_ee <- function(radar, time, ...,
       class = "getRad_error_get_pvol_ee_differing_n_files"
     )
   }
-  req <- httr2::request("https://avaandmed.keskkonnaportaal.ee/_vti_bin/RmApi.svc/active/items/") |>
-    req_user_agent_getrad() |>
-    httr2::req_url_path_append(files$documents[[1]]$id) |>
-    httr2::req_url_path_append("files/0") |>
-    req_retry_getrad() |>
-    httr2::req_perform(path = tempfile(fileext = ".h5"), error_call = call)
-  pvol <- bioRad::read_pvolfile(req$body, ...)
-  file.remove(req$body)
+  pvol <- withr::with_tempfile("file", fileext = ".h5", {
+    req <- httr2::request("https://avaandmed.keskkonnaportaal.ee/_vti_bin/RmApi.svc/active/items/") |>
+      req_user_agent_getrad() |>
+      httr2::req_url_path_append(files$documents[[1]]$id) |>
+      httr2::req_url_path_append("files/0") |>
+      req_retry_getrad() |>
+      httr2::req_perform(path = file, error_call = call)
+    bioRad::read_pvolfile(req$body, ...)
+  })
   return(pvol)
 }

R/get_pvol_fi.R

@@ -13,17 +13,17 @@ get_pvol_fi <- function(radar, time, ..., call = rlang::caller_env()) {
         "{strftime(time,'%Y', tz='UTC')}/{strftime(time,'%m', tz='UTC')}/{strftime(time,'%d', tz='UTC')}/{radar}/{strftime(time,'%Y%m%d%H%M', tz='UTC')}_{radar}_PVOL.h5"
       ))
     )
-
-  req <- req |>
-    httr2::req_perform(path = tempfile(fileext = ".h5"), error_call = call)
-  rlang::check_installed("rhdf5", "To adjust the polar volume files for Finish data.", call = call)
-  hdf_connection <- rhdf5::H5Fopen(req$body)
-  group <- rhdf5::H5Gopen(hdf_connection, "what")
-  rhdf5::h5writeAttribute("PVOL", group, "object")
-  rhdf5::H5Fclose(hdf_connection)
-  rhdf5::H5Gclose(group)
-  pvol <- bioRad::read_pvolfile(req$body, ...)
-  file.remove(req$body)
+  pvol <- withr::with_tempfile("file", fileext = ".h5", {
+    req <- req |>
+      httr2::req_perform(path = file, error_call = call)
+    rlang::check_installed("rhdf5", "To adjust the polar volume files for Finish data.", call = call)
+    hdf_connection <- rhdf5::H5Fopen(req$body)
+    group <- rhdf5::H5Gopen(hdf_connection, "what")
+    rhdf5::h5writeAttribute("PVOL", group, "object")
+    rhdf5::H5Fclose(hdf_connection)
+    rhdf5::H5Gclose(group)
+    bioRad::read_pvolfile(req$body, ...)
+  })
   return(pvol)
 }
 # https://en.ilmatieteenlaitos.fi/radar-data-on-aws-s3