Merge branch 'main' into sf-related-pkgs

EMODnet · Feb 28, 2024 · 4480102 · 4480102
2 parents 8dc3969 + 3ef9dbe
commit 4480102
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -16,3 +16,4 @@
 ^Meta$
 ^attic$
 ^codemeta\.json$
+^vignettes/EMODnetWFS\.Rmd\.orig$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,7 +4,7 @@ Version: 2.0.1.9001
 Authors@R: c(
     person("Anna", "Krystalli", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-2378-4915")),
-    person("Salvador", "Fernández-Bejarano", , "[email protected]", role = c("ctb", "cre"),
+    person("Salvador", "Fernández-Bejarano", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0535-7677")),
     person("Thomas J", "Webb", , "[email protected]", role = "ctb"),
     person("European Marine Observation Data Network (EMODnet) Biology project", "European Commission's Directorate - General for Maritime Affairs and Fisheries (DG MARE)", , "[email protected]", role = "cph"),
@@ -15,7 +15,8 @@ Authors@R: c(
 Description: Access and interrogate EMODnet Web Feature Service data
     through R.
 License: MIT + file LICENSE
-URL: https://emodnet.github.io/EMODnetWFS/, https://github.com/EMODnet/EMODnetWFS
+URL: https://emodnet.github.io/EMODnetWFS/,
+    https://github.com/EMODnet/EMODnetWFS
 BugReports: https://github.com/EMODnet/EMODnetWFS/issues
 Depends: 
     R (>= 3.6.0)
@@ -28,7 +29,7 @@ Imports:
     lifecycle,
     magrittr,
     memoise,
-    ows4R (>= 0.3),
+    ows4R (>= 0.3-4),
     purrr,
     rlang,
     sf,
@@ -48,14 +49,15 @@ Suggests:
     testthis,
     webmockr,
     withr
+VignetteBuilder: 
+    knitr
 Remotes: 
     eblondel/ows4R,
     nealrichardson/httptest,
     r-spatial/mapview
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
-VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 SystemRequirements: C++11, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>=

diff --git a/R/EMODnetWFS-package.R b/R/EMODnetWFS-package.R
@@ -15,19 +15,33 @@ emodnetwfs_user_agent <- function() {
   version <- as.character(utils::packageVersion("EMODnetWFS"))
 
   if (nzchar(Sys.getenv("EMODNETWFS_CI"))) {
-    return(sprintf("EMODnetWFS R package %s CI https://github.com/EMODnet/EMODnetWFS", version))
+    return(
+      sprintf(
+        "EMODnetWFS R package %s CI https://github.com/EMODnet/EMODnetWFS",
+        version
+      )
+    )
   }
 
   gh_username <- try(whoami::gh_username(), silent = TRUE)
-  if (!inherits(gh_username, "try-error") && gh_username %in% emodnetwfs_collaborators()) {
-    return(sprintf("EMODnetWFS R package %s DEV https://github.com/EMODnet/EMODnetWFS", version))
+  if (!inherits(gh_username, "try-error") &&
+    gh_username %in% emodnetwfs_collaborators()) {
+    return(
+      sprintf(
+        "EMODnetWFS R package %s DEV https://github.com/EMODnet/EMODnetWFS",
+        version
+      )
+    )
   }
 
-  sprintf("EMODnetWFS R package %s https://github.com/EMODnet/EMODnetWFS", version)
+  sprintf(
+    "EMODnetWFS R package %s https://github.com/EMODnet/EMODnetWFS",
+    version
+  )
 }
 
 globalVariables(c("layer_name", "n"))
 
 release_bullets <- function() {
-	c('update vignette with knitr::knit("vignettes/EMODnetWFS.Rmd.orig", output = "vignettes/EMODnetWFS.Rmd")')
+  c('update vignette with knitr::knit("vignettes/EMODnetWFS.Rmd.orig", output = "vignettes/EMODnetWFS.Rmd")')
 }
diff --git a/R/client.R b/R/client.R
@@ -2,20 +2,28 @@
 #'
 #' @param service the EMODnet OGC WFS service name.
 #' For available services, see [`emodnet_wfs()`].
-#' @param service_version `r lifecycle::badge('deprecated')` the WFS service version. Now always "2.0.0".
-#' @param logger the logger. Either `NULL` (no logging info), `"INFO"` (log about ows4R requests)
+#' @param service_version `r lifecycle::badge('deprecated')`
+#' the WFS service version. Now always "2.0.0".
+#' @param logger the logger. Either `NULL` (no logging info), `"INFO"`
+#' (log about ows4R requests)
 #' or `"DEBUG"` (including curl details).
 #'
-#' @return An [`ows4R::WFSClient`] R6 object with methods for interfacing an OGC Web Feature Service.
+#' @return An [`ows4R::WFSClient`] R6 object with methods for interfacing an
+#' OGC Web Feature Service.
 #' @export
 #'
 #' @seealso `WFSClient` in package `ows4R`.
 #' @examples
 #' \dontrun{
 #' wfs <- emodnet_init_wfs_client(service = "bathymetry")
 #' }
-emodnet_init_wfs_client <- function(service, service_version = NULL, logger = NULL) {
-  deprecate_message_service_version(service_version, "deprecate_message_service_version")
+emodnet_init_wfs_client <- function(service,
+                                    service_version = NULL,
+                                    logger = NULL) {
+  deprecate_message_service_version(
+    service_version,
+    "deprecate_message_service_version"
+  )
 
   check_service_name(service)
 
@@ -97,12 +105,18 @@ check_service <- function(request) {
   if (httr::http_error(request)) {
     cli_alert_danger("HTTP Status: {httr::http_status(request)$message}")
 
-    is_monitor_up <- !is.null(curl::nslookup("monitor.emodnet.eu", error = FALSE))
+    is_monitor_up <- !is.null(
+      curl::nslookup("monitor.emodnet.eu", error = FALSE)
+    )
     if (interactive() && is_monitor_up) {
-      browse_monitor <- utils::askYesNo("Browse the EMODnet OGC monitor?", FALSE, prompts = "yes/no/cancel")
+      browse_monitor <- utils::askYesNo(
+        "Browse the EMODnet OGC monitor?",
+        FALSE,
+        prompts = "yes/no/cancel"
+      )
       if (is.na(browse_monitor)) browse_monitor <- FALSE
       if (browse_monitor) {
-        utils::browseURL("https://monitor.emodnet.eu/resources?lang=en&resource_type=OGC:WFS")
+        utils::browseURL("https://monitor.emodnet.eu/resources?lang=en&resource_type=OGC:WFS") # nolint
       }
     }
 
@@ -115,7 +129,7 @@ check_service <- function(request) {
     cli::cli_abort(
       c(
         "An exception has occurred.",
-        i = "Please raise an issue in {packageDescription('EMODnetWFS')$BugReports}"
+        i = "Please raise an issue in {packageDescription('EMODnetWFS')$BugReports}" # nolint
       )
     )
   }

diff --git a/R/info.R b/R/info.R
@@ -32,11 +32,15 @@
 #' @importFrom memoise memoise
 #' @details To minimize the number of requests sent to webservices,
 #' these functions use `memoise` to cache results inside the active R session.
-#' To clear the cache, re-start R or run `memoise::forget(emodnet_get_wfs_info)`/`memoise::forget(emodnet_get_layer_info)`.
+#' To clear the cache, re-start R or
+#' run `memoise::forget(emodnet_get_wfs_info)`/
+#' `memoise::forget(emodnet_get_layer_info)`.
 #' @export
 emodnet_get_layer_info <- memoise::memoise(.emodnet_get_layer_info)
 
-.emodnet_get_wfs_info <- function(wfs = NULL, service = NULL, service_version = NULL) {
+.emodnet_get_wfs_info <- function(wfs = NULL,
+                                  service = NULL,
+                                  service_version = NULL) {
   deprecate_message_service_version(service_version, "emodnet_get_wfs_info")
 
   if (is.null(wfs) && is.null(service)) {
@@ -59,7 +63,10 @@ emodnet_get_layer_info <- memoise::memoise(.emodnet_get_layer_info)
     service_url = capabilities$getUrl(),
     layer_name = purrr::map_chr(capabilities$getFeatureTypes(), ~ .x$getName()),
     title = purrr::map_chr(capabilities$getFeatureTypes(), ~ .x$getTitle()),
-    abstract = purrr::map_chr(capabilities$getFeatureTypes(), ~ get_abstract_null(.x)),
+    abstract = purrr::map_chr(
+      capabilities$getFeatureTypes(),
+      ~ get_abstract_null(.x)
+    ),
     class = purrr::map_chr(capabilities$getFeatureTypes(), ~ .x$getClassName()),
     format = purrr::map_chr(capabilities$getFeatureTypes(), guess_layer_format)
   ) %>%
@@ -71,11 +78,14 @@ emodnet_get_layer_info <- memoise::memoise(.emodnet_get_layer_info)
 }
 #' Get WFS available layer information
 #'
-#' @param wfs A `WFSClient` R6 object with methods for interfacing an OGC Web Feature Service.
+#' @param wfs A `WFSClient` R6 object with methods for interfacing an
+#'  OGC Web Feature Service.
 #' @inheritParams emodnet_init_wfs_client
-#' @return a tibble containing metadata on each layer available from the service.
+#' @return a tibble containing metadata on each layer available from the
+#'  service.
 #' @export
-#' @describeIn emodnet_get_wfs_info Get info on all layers from am EMODnet WFS service.
+#' @describeIn emodnet_get_wfs_info Get info on all layers from
+#' an EMODnet WFS service.
 #' @examples
 #' \dontrun{
 #' emodnet_get_wfs_info(service = "bathymetry")

diff --git a/R/layer_attributes.R b/R/layer_attributes.R
@@ -5,18 +5,25 @@
 #' @param layer character sting of layer name. To get info on layers, including
 #' `layer_name` use [emodnet_get_wfs_info()].
 #'
-#' @return output of `summary()` on the attributes (variables) in a given layer for a given service.
+#' @return output of `summary()` on the attributes (variables) in a given layer
+#' for a given service.
 #' @export
 #'
 #' @examples
 #' \dontrun{
-#' layer_attributes_summarise(service = "human_activities", layer = "maritimebnds")
+#' layer_attributes_summarise(
+#'   service = "human_activities",
+#'   layer = "maritimebnds"
+#' )
 #' }
 layer_attributes_summarise <- function(wfs = NULL,
                                        service = NULL,
                                        service_version = NULL,
                                        layer) {
-  deprecate_message_service_version(service_version, "layer_attributes_summarise")
+  deprecate_message_service_version(
+    service_version,
+    "layer_attributes_summarise"
+  )
   summary(
     layer_attributes_tbl(
       wfs = wfs,
@@ -37,12 +44,18 @@ layer_attributes_summarise <- function(wfs = NULL,
 #'
 #' @examples
 #' \dontrun{
-#' layer_attribute_descriptions(service = "human_activities", layer = "maritimebnds")
+#' layer_attribute_descriptions(
+#'   service = "human_activities",
+#'   layer = "maritimebnds"
+#' )
 #' }
 layer_attribute_descriptions <- function(wfs = NULL,
                                          service = NULL,
                                          service_version = NULL, layer) {
-  deprecate_message_service_version(service_version, "layer_attribute_descriptions")
+  deprecate_message_service_version(
+    service_version,
+    "layer_attribute_descriptions"
+  )
 
   wfs <- wfs %||% emodnet_init_wfs_client(service)
   check_wfs(wfs)
@@ -62,13 +75,19 @@ layer_attribute_descriptions <- function(wfs = NULL,
 #'
 #' @examples
 #' \dontrun{
-#' layer_attributes_get_names(service = "human_activities", layer = "maritimebnds")
+#' layer_attributes_get_names(
+#'   service = "human_activities",
+#'   layer = "maritimebnds"
+#' )
 #' }
 layer_attributes_get_names <- function(wfs = NULL,
                                        service = NULL,
                                        service_version = NULL,
                                        layer) {
-  deprecate_message_service_version(service_version, "layer_attributes_get_names")
+  deprecate_message_service_version(
+    service_version,
+    "layer_attributes_get_names"
+  )
 
   layer_attribute_descriptions(
     wfs = wfs,
@@ -85,7 +104,8 @@ layer_attributes_get_names <- function(wfs = NULL,
 #' @inheritParams emodnet_init_wfs_client
 #' @inheritParams emodnet_get_wfs_info
 #'
-#' @return Detailed summary of individual attribute (variable). Particularly useful for inspecting
+#' @return Detailed summary of individual attribute (variable). Particularly
+#' useful for inspecting
 #' factor or character variable levels or unique values.
 #' @export
 #'
@@ -116,7 +136,10 @@ layer_attribute_inspect <- function(wfs = NULL,
     choices = layer_attributes_get_names(wfs, layer = layer)
   )
 
-  attribute_vector <- wfs$getFeatures(namespaced_layer, PROPERTYNAME = attribute)[[attribute]]
+  attribute_vector <- wfs$getFeatures(
+    namespaced_layer,
+    PROPERTYNAME = attribute
+  )[[attribute]]
 
   if (inherits(attribute_vector, "sfc")) {
     attribute_type <- "geometry"
@@ -141,9 +164,12 @@ layer_attribute_inspect <- function(wfs = NULL,
 #' @inheritParams emodnet_get_wfs_info
 #' @inheritParams layer_attributes_summarise
 #'
-#' @return tibble of layer attribute (variable) values with geometry column removed.
-#' @details Request excluding spatial information can be significantly faster. Can be
-#' useful for inspecting attribute values and constructing feature filters for more
+#' @return tibble of layer attribute (variable) values
+#' with geometry column removed.
+#' @details Request excluding spatial information can be significantly faster.
+#' Can be
+#' useful for inspecting attribute values and constructing feature filters
+#' for more
 #' targeted and faster layer download.
 #' @export
 #'
@@ -168,7 +194,10 @@ layer_attributes_tbl <- function(wfs = NULL,
   attributes <- layer_attributes_get_names(wfs, layer = layer)
   attributes <- attributes[attributes != get_layer_geom_name(layer, wfs)]
 
-  wfs$getFeatures(namespaced_layer, PROPERTYNAME = paste(attributes, collapse = ",")) %>%
+  wfs$getFeatures(
+    namespaced_layer,
+    PROPERTYNAME = paste(attributes, collapse = ",")
+  ) %>%
     sf::st_drop_geometry() %>%
     tibble::as_tibble()
 }
@@ -196,7 +225,9 @@ get_layer_geom_name <- function(layer, wfs) {
   desc$name[desc$type == "geometry"]
 }
 
-get_layer_default_crs <- function(layer, wfs, output = c("crs", "epsg.text", "epsg.num")) {
+get_layer_default_crs <- function(layer,
+                                  wfs,
+                                  output = c("crs", "epsg.text", "epsg.num")) {
   check_wfs(wfs)
   output <- match.arg(output, several.ok = FALSE)
 
@@ -211,7 +242,10 @@ get_layer_default_crs <- function(layer, wfs, output = c("crs", "epsg.text", "ep
     return(crs)
   }
 
-  epsg.text <- regmatches(crs$input, regexpr("epsg\\:[[:digit:]]{4}", crs$input))
+  epsg.text <- regmatches(
+    crs$input,
+    regexpr("epsg\\:[[:digit:]]{4}", crs$input)
+  )
   if (output == "epsg.text") {
     return(epsg.text)
   }
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,3 +16,4 @@ @@
     ^Meta$
     ^attic$
     ^codemeta\.json$
+    ^vignettes/EMODnetWFS\.Rmd\.orig$