Replace rjson dependency by jsonlite

There are a couple of reasons for this change.  First, rjson depends
on a recent version of R (>= 4.4.0), which is the current released
minor version, while jsonlite should be able to work with older
versions.  Second, as of the time of this writing, the CRAN task view
for Web Technologies and Services recommends using the jsonlite
package.

https://cran.r-project.org/web/views/WebTechnologies.html

Also, fromJSON() in jsonlite coerces the records in the response to a
data.frame by default, which is in principle quite convenient (and
gtools::smartbind() does not seem to be needed anymore), although it
is possible that in some cases this gives unexpected results.  Some
new bugs could appear because of this.

DESCRIPTION

@@ -22,9 +22,8 @@ URL: https://docs.ropensci.org/paleobioDB/,
 BugReports: https://github.com/ropensci/paleobioDB/issues
 Imports:
     curl,
-    gtools,
+    jsonlite,
     maps,
-    rjson,
     terra
 Suggests:
     roxygen2,

NEWS.md

@@ -1,3 +1,15 @@
+paleobioDB 1.0.0.9000
+=====================
+
+### DOCUMENTATION FIXES
+
+* In `pbdb_scales()`, at least one parameter needs to be specified
+  now, so the examples in the documentation were updated accordingly.
+
+### OTHER CHANGES
+
+* The `rjson` dependency was replaced by `jsonlite`.
+
 paleobioDB 1.0.0
 ================
 

R/network.R

@@ -76,7 +76,7 @@
 #' @returns data frame
 #' @noRd
 .parse_raw_data <- function(raw_data) {
-  data_list <- rjson::fromJSON(raw_data)
+  data_list <- jsonlite::fromJSON(raw_data)
 
   if ("warnings" %in% names(data_list)) {
     # Enumerate warnings that were returned by the PBDB API
@@ -93,31 +93,16 @@
     )
   }
 
-  df <- .make_data_frame(data_list$records)
-  df
-}
-
-
-#' .make_data_frame
-#'
-#' Makes a data frame from a list of lists
-#'
-#' @param reg_list data rows as a list of lists
-#' @returns data frame
-#' @noRd
-.make_data_frame <- function(reg_list) {
-  if (length(reg_list) == 0) {
+  if (length(data_list$records) == 0) {
     warning("The PBDB API returned no records for this query.", call. = FALSE)
     return(data.frame())
   }
 
-  dfr_rows <- lapply(reg_list, function(reg) {
-    as.data.frame(lapply(reg, .collapse_array_columns_map))
-  })
+  if (!is.data.frame(data_list$records)) {
+    stop("The records in the response were not coerced to a data.frame")
+  }
 
-  dfr <- do.call(gtools::smartbind, dfr_rows)
-  dfr <- .convert_data_frame_columns(dfr)
-  dfr
+  .convert_data_frame_columns(data_list$records)
 }
 
 #' .build_query_string
@@ -144,26 +129,6 @@
   qs
 }
 
-#' .collapse_array_columns_map
-#'
-#' Maps multivalue elements to semicolon separated strings
-#'
-#' @param element a vector representing some data field
-#' @returns a string with the elements of the provided vector separated
-#'   by semicolons if it has more than one element or the vector as it
-#'   was passed to the function if it has length one
-#' @noRd
-.collapse_array_columns_map <- function(element) {
-  if (length(element) > 1) {
-    mapped <- paste(element, collapse = ";")
-  } else {
-    mapped <- element
-  }
-
-  mapped
-}
-
-
 #' .convert_data_frame_columns
 #'
 #' Converts some columns (lng, lat) from character to numeric.  This

tests/testthat/test-network.R

@@ -38,28 +38,23 @@ test_that(".parse_raw_data() replicates warnings from the API", {
   )
 })
 
-test_that(".make_data_frame() warns the user if no records are returned", {
+test_that(".parse_raw_data() warns the user if no records are returned", {
+  resp <- readRDS(test_path("fixtures", "no_records_resp.rds"))
+  raw_data <- .extract_response_body(resp)
   expect_warning(
-    .make_data_frame(list()),
+    .parse_raw_data(raw_data),
     regexp = "The PBDB API returned no records for this query."
   )
 })
 
-test_that(".make_data_frame() returns a data frame", {
+test_that(".parse_raw_data() returns a data frame", {
   resp <- readRDS(test_path("fixtures", "valid_id_resp.rds"))
   raw_data <- .extract_response_body(resp)
-  data_list <- rjson::fromJSON(raw_data)
-  df <- .make_data_frame(data_list$records)
+  df <- .parse_raw_data(raw_data)
   expect_s3_class(df, "data.frame")
   expect_identical(
     names(df),
     c("oid", "cid", "tna", "rnk", "tid", "oei",
       "eag", "lag", "rid", "lng", "lat")
   )
 })
-
-test_that(".collapse_array_columns_map() returns a length one character", {
-  s <- .collapse_array_columns_map(1:3)
-  expect_length(s, 1)
-  expect_equal(s, "1;2;3")
-})