Merge pull request #33 from atorus-research/yyjsonr_switch

Yyjsonr switch

DESCRIPTION

@@ -21,13 +21,14 @@ Language: en-US
 License: Apache License (>= 2)
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
-Depends: R (>= 3.5)
+RoxygenNote: 7.3.1
+Depends: R (>= 4.0)
 Imports:
- jsonlite (>= 1.8.0),
+ yyjsonr (>= 0.1.18),
  jsonvalidate (>= 1.3.1)
 Suggests:
  testthat (>= 2.1.0),
+ jsonlite (>= 1.8.0),
  knitr,
  haven,
  rmarkdown,

NAMESPACE

@@ -23,8 +23,12 @@ export(set_source_system)
 export(set_study_oid)
 export(validate_dataset_json)
 export(write_dataset_json)
-importFrom(jsonlite,fromJSON)
-importFrom(jsonlite,toJSON)
 importFrom(jsonvalidate,json_validate)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,tail)
+importFrom(yyjsonr,opts_read_json)
+importFrom(yyjsonr,opts_write_json)
+importFrom(yyjsonr,read_json_file)
+importFrom(yyjsonr,read_json_str)
+importFrom(yyjsonr,write_json_file)
+importFrom(yyjsonr,write_json_str)

R/dataset_metadata.R

@@ -95,7 +95,7 @@ set_item_data <- function(x, .data, ...) {
 
  # Insert into object in proper spots
  x[[1]][['records']] <- records
- x[[1]][['itemData']] <- item_data
+ x[[1]][['itemData']] <- unname(item_data)
  x
 }
 

R/read_dataset_json.R

@@ -23,19 +23,32 @@
 #' dat <- read_dataset_json(js)
 read_dataset_json <- function(file) {
 
+ json_opts <- yyjsonr::opts_read_json(
+ promote_num_to_string = TRUE
+ )
+
  if (path_is_url(file)) {
  # Url?
  file_contents <- read_from_url(file)
+ ds_json <- yyjsonr::read_json_str(
+ file_contents,
+ opts = json_opts
+ )
  } else if (file.exists(file)) {
  # File on disk?
- file_contents <- readLines(file)
+ ds_json <- yyjsonr::read_json_file(
+ file,
+ opts = json_opts
+ )
  } else {
  # Direct file contents?
- file_contents <- file
+ ds_json <- yyjsonr::read_json_str(
+ file,
+ opts = json_opts
+ )
  }
 
- # Read the file and convert to datasetjson object
- ds_json <- jsonlite::fromJSON(file_contents)
+
 
  # Pull the object out with a lot of assumptions because the format has already
  # been validated

R/write_dataset_json.R

@@ -32,18 +32,23 @@ write_dataset_json <- function(x, file, pretty=FALSE) {
  }
 
  # Create the JSON text
- js <- jsonlite::toJSON(
- x,
- dataframe = "values",
- na = "null",
+ json_opts <- yyjsonr::opts_write_json(
+ pretty = pretty,
  auto_unbox = TRUE,
-  pretty = pretty)
+ )
 
  if (!missing(file)) {
  # Write file to disk
- cat(js, "\n", file = file)
+ yyjsonr::write_json_file(
+ x,
+ filename = file,
+ opts = json_opts
+ )
  } else {
  # Print to console
- js
+ yyjsonr::write_json_str(
+ x,
+ opts = json_opts
+ )
  }
 }

R/zzz.R

@@ -1,5 +1,5 @@
 #' @importFrom jsonvalidate json_validate
-#' @importFrom jsonlite fromJSON toJSON
+#' @importFrom yyjsonr opts_write_json opts_read_json write_json_file write_json_str read_json_str read_json_file
 #' @importFrom tools file_path_sans_ext
 #' @importFrom utils tail
 NULL

tests/testthat/test-datasetjson.R

@@ -49,10 +49,10 @@ test_that("datasetjson object builds with minimal defaults", {
  expect_equal(ds_json$clinicalData$itemGroupData$IG.IRIS$items, iris_items_list)
 
  # Verify that data are attached properly with ITEMGRPUPSEQ attached
- iris_test <- cbind(
+ iris_test <- unname(cbind(
  ITEMGROUPDATASEQ = 1:nrow(iris),
  iris
- )
+ ))
 
  expect_equal(ds_json$clinicalData$itemGroupData$IG.IRIS$itemData, iris_test)
 })