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EMODnet · Mar 15, 2024 · c2c2248 · c2c2248
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Showing 7 changed files with 99 additions and 104 deletions.
diff --git a/EMODnetWFS.Rproj b/EMODnetWFS.Rproj
@@ -5,7 +5,7 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
-UseSpacesForTab: No
+UseSpacesForTab: Yes
 NumSpacesForTab: 4
 Encoding: UTF-8
 

diff --git a/R/client.R b/R/client.R
@@ -18,49 +18,49 @@
 #' 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"
-	)
+                                    service_version = NULL,
+                                    logger = NULL) {
+  deprecate_message_service_version(
+    service_version,
+    "deprecate_message_service_version"
+  )
 
-	check_service_name(service)
+  check_service_name(service)
 
-	service_url <- get_service_url(service)
+  service_url <- get_service_url(service)
 
-	wfs <- suppressWarnings(
-		ows4R::WFSClient$new(
-			service_url,
-			serviceVersion = "2.0.0",
-			headers = c("User-Agent" = emodnetwfs_user_agent()),
-			logger = logger
-		)
-	)
+  wfs <- suppressWarnings(
+    ows4R::WFSClient$new(
+      service_url,
+      serviceVersion = "2.0.0",
+      headers = c("User-Agent" = emodnetwfs_user_agent()),
+      logger = logger
+    )
+  )
 
-	check_wfs(wfs)
-	cli_alert_success("WFS client created successfully")
-	cli_alert_info("Service: {.val {wfs$getUrl()}}")
-	cli_alert_info("Version: {.val {wfs$getVersion()}}")
+  check_wfs(wfs)
+  cli_alert_success("WFS client created successfully")
+  cli_alert_info("Service: {.val {wfs$getUrl()}}")
+  cli_alert_info("Version: {.val {wfs$getVersion()}}")
 
-	wfs
+  wfs
 }
 
 check_service_name <- function(service) {
-	checkmate::assert_choice(service, emodnet_wfs()$service_name)
+  checkmate::assert_choice(service, emodnet_wfs()$service_name)
 }
 
 check_wfs <- function(wfs) {
-	checkmate::assertR6(
-		wfs,
-		classes = c("WFSClient", "OWSClient", "OGCAbstractObject", "R6")
-	)
+  checkmate::assertR6(
+    wfs,
+    classes = c("WFSClient", "OWSClient", "OGCAbstractObject", "R6")
+  )
 }
 
 get_service_url <- function(service) {
-	emodnet_wfs()$service_url[emodnet_wfs()$service_name == service]
+  emodnet_wfs()$service_url[emodnet_wfs()$service_name == service]
 }
 
 get_service_name <- function(service_url) {
-	emodnet_wfs()$service_name[emodnet_wfs()$service_url == service_url]
+  emodnet_wfs()$service_name[emodnet_wfs()$service_url == service_url]
 }
diff --git a/README.Rmd b/README.Rmd
@@ -172,12 +172,11 @@ rerddap::ed_datasets(url = erddap_url)
 
 rerddap::ed_search(query = "vessel density", url = erddap_url)
 
-human_activities_data_info <- rerddap::info(datasetid = 'humanactivities_9f8a_3389_f08a', url = erddap_url)
+human_activities_data_info <- rerddap::info(datasetid = "humanactivities_9f8a_3389_f08a", url = erddap_url)
 human_activities_data_info
 
-year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c('2020-03-18', '2020-03-19'))
+year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c("2020-03-18", "2020-03-19"))
 head(year_2020_gridded_data$data)
-
 ```
 
 

diff --git a/tests/testthat/test-info.R b/tests/testthat/test-info.R
@@ -39,5 +39,5 @@ test_that("emodnet_get_layer_info() works", {
 })
 
 test_that("emodnet_get_wfs_info() errors well", {
-	expect_snapshot(emodnet_get_wfs_info(), error = TRUE)
+  expect_snapshot(emodnet_get_wfs_info(), error = TRUE)
 })
diff --git a/tests/testthat/test-layer_attributes.R b/tests/testthat/test-layer_attributes.R
@@ -1,80 +1,79 @@
 test_that("layer attributes stuff works", {
-	skip_if_offline()
-	wfs <- create_biology_wfs()
+  skip_if_offline()
+  wfs <- create_biology_wfs()
 
-	with_mock_dir("biology-layers", {
-		layer_attr <- layer_attributes_get_names(wfs, layer = "mediseh_zostera_m_pnt")
-		expect_identical(layer_attr, c("id", "country", "the_geom"))
+  with_mock_dir("biology-layers", {
+    layer_attr <- layer_attributes_get_names(wfs, layer = "mediseh_zostera_m_pnt")
+    expect_identical(layer_attr, c("id", "country", "the_geom"))
 
-		layer_attr_desc <- layer_attribute_descriptions(
-			wfs,
-			layer = "mediseh_zostera_m_pnt"
-		)
-		expect_snapshot_output(layer_attr_desc)
+    layer_attr_desc <- layer_attribute_descriptions(
+      wfs,
+      layer = "mediseh_zostera_m_pnt"
+    )
+    expect_snapshot_output(layer_attr_desc)
 
-		country <- layer_attribute_inspect(
-			wfs,
-			layer = "mediseh_zostera_m_pnt",
-			attribute = "country"
-		)
-		expect_s3_class(country, c("tabyl", "data.frame"))
-		expect_named(country, c(".", "n", "percent"))
-		expect_gt(nrow(country), 1L)
+    country <- layer_attribute_inspect(
+      wfs,
+      layer = "mediseh_zostera_m_pnt",
+      attribute = "country"
+    )
+    expect_s3_class(country, c("tabyl", "data.frame"))
+    expect_named(country, c(".", "n", "percent"))
+    expect_gt(nrow(country), 1L)
 
-		the_geom <- layer_attribute_inspect(
-			wfs,
-			layer = "mediseh_zostera_m_pnt",
-			attribute = "the_geom"
-		)
-		expect_s3_class(the_geom, c("sfc_POINT", "sfc"))
+    the_geom <- layer_attribute_inspect(
+      wfs,
+      layer = "mediseh_zostera_m_pnt",
+      attribute = "the_geom"
+    )
+    expect_s3_class(the_geom, c("sfc_POINT", "sfc"))
 
-		id <- layer_attribute_inspect(
-			wfs,
-			layer = "mediseh_zostera_m_pnt",
-			attribute = "id"
-		)
-		expect_s3_class(id, c("summaryDefault", "table"))
-		expect_named(id, c("Min.", "1st Qu.", "Median", "Mean", "3rd Qu.", "Max."))
-		expect_length(id, 6L)
+    id <- layer_attribute_inspect(
+      wfs,
+      layer = "mediseh_zostera_m_pnt",
+      attribute = "id"
+    )
+    expect_s3_class(id, c("summaryDefault", "table"))
+    expect_named(id, c("Min.", "1st Qu.", "Median", "Mean", "3rd Qu.", "Max."))
+    expect_length(id, 6L)
 
-		attr_summary <- layer_attributes_summarise(
-			wfs,
-			layer = "mediseh_zostera_m_pnt"
-		)
+    attr_summary <- layer_attributes_summarise(
+      wfs,
+      layer = "mediseh_zostera_m_pnt"
+    )
 
-		expect_s3_class(attr_summary, "table")
-		expect_identical(
-			attr_summary[, "  country"][2:3],
-			structure(c("Class :character  ", "Mode  :character  "), .Names = c(
-				"",
-				""
-			))
-		)
-		expect_identical(
-			attr_summary[, 2][1],
-			structure("Min.   :0  ", .Names = "")
-		)
+    expect_s3_class(attr_summary, "table")
+    expect_identical(
+      attr_summary[, "  country"][2:3],
+      structure(c("Class :character  ", "Mode  :character  "), .Names = c(
+        "",
+        ""
+      ))
+    )
+    expect_identical(
+      attr_summary[, 2][1],
+      structure("Min.   :0  ", .Names = "")
+    )
 
-		crs1 <- get_layer_default_crs(
-			layer = "mediseh_zostera_m_pnt",
-			wfs,
-			output = "epsg.text"
-		)
-		expect_identical(crs1, "epsg:4326")
+    crs1 <- get_layer_default_crs(
+      layer = "mediseh_zostera_m_pnt",
+      wfs,
+      output = "epsg.text"
+    )
+    expect_identical(crs1, "epsg:4326")
 
-		crs2 <- get_layer_default_crs(
-			layer = "mediseh_zostera_m_pnt",
-			wfs,
-			output = "epsg.num"
-		)
-	})
-	expect_identical(crs2, 4326)
-
-	crs3 <- get_layer_default_crs(
-		layer = "mediseh_zostera_m_pnt",
-		wfs,
-		output = "crs"
-	)
-	expect_s3_class(crs3, "crs")
+    crs2 <- get_layer_default_crs(
+      layer = "mediseh_zostera_m_pnt",
+      wfs,
+      output = "epsg.num"
+    )
+  })
+  expect_identical(crs2, 4326)
 
+  crs3 <- get_layer_default_crs(
+    layer = "mediseh_zostera_m_pnt",
+    wfs,
+    output = "crs"
+  )
+  expect_s3_class(crs3, "crs")
 })
diff --git a/vignettes/articles/ecql_filtering.Rmd b/vignettes/articles/ecql_filtering.Rmd
@@ -270,7 +270,6 @@ emodnet_get_layers(
 Let's say we also want to restrict the features returned those having `shape_length` > 1. We can include an additional condition which must be met using an `AND` statement.
 
 ```{r, eval=FALSE}
-
 filter_sf1 <- emodnet_get_layers(
   wfs = wfs,
   layers = "seabed_substrate_1m",

diff --git a/vignettes/articles/request-params.Rmd b/vignettes/articles/request-params.Rmd
@@ -132,7 +132,6 @@ To limit data returned to the single attribute `"country"` from just 3 features,
 Note that when limiting data to specific attributes, all other columns are returned as `NA` (including any spatial, in this case `the_geom`, column).
 
 ```{r}
-
 emodnet_get_layers(
   wfs = wfs,
   layers = "maritimebnds",
@@ -145,7 +144,6 @@ emodnet_get_layers(
 To limit to multiple attributes, separate each attribute name in the character string supplied to `propertyName` by a comma.
 
 ```{r}
-
 emodnet_get_layers(
   wfs = wfs,
   layers = "maritimebnds",