From 466823b6119af2038298c5d92a1ce7198ecce4ab Mon Sep 17 00:00:00 2001 From: "mike.stackhouse" Date: Thu, 14 Sep 2023 13:40:00 +0000 Subject: [PATCH 1/4] Description updates per CRAN comments. --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index cca3fe7..443dd75 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -13,7 +13,7 @@ Authors@R: c( email = "nmasel@its.jnj.com", role = "aut") ) -Description: R package for reading and writing CDISC Dataset JSON files. +Description: Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) . URL: https://github.com/atorus-research/datasetjson BugReports: https://github.com/atorus-research/datasetjson/issues Encoding: UTF-8 From e6a54f485e6dc2b9b4b35f5ee571acade883230d Mon Sep 17 00:00:00 2001 From: "mike.stackhouse" Date: Thu, 14 Sep 2023 13:40:25 +0000 Subject: [PATCH 2/4] eliminate unsuppressable messages --- R/validate_dataset_json.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/validate_dataset_json.R b/R/validate_dataset_json.R index 8190f1a..c511bfe 100644 --- a/R/validate_dataset_json.R +++ b/R/validate_dataset_json.R @@ -22,10 +22,10 @@ validate_dataset_json <- function(x) { v <- jsonvalidate::json_validate(x, schema_1_0_0, engine="ajv", verbose=TRUE) if (!v) { - cat("File contains errors!") + warning("File contains errors!") return(attr(v, 'errors')) } else { - cat("File is valid per the Dataset JSON v1.0.0 schema\n") + message("File is valid per the Dataset JSON v1.0.0 schema\n") data.frame( instancePath = character(), schemaPath = character(), From fd4c22ba131c669243d0ebda6d05b7b9152e3392 Mon Sep 17 00:00:00 2001 From: "mike.stackhouse" Date: Thu, 14 Sep 2023 13:40:34 +0000 Subject: [PATCH 3/4] Add return value --- R/write_dataset_json.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/write_dataset_json.R b/R/write_dataset_json.R index 8ef372a..9674751 100644 --- a/R/write_dataset_json.R +++ b/R/write_dataset_json.R @@ -4,7 +4,7 @@ #' @param file File path to save Dataset JSON file #' @param pretty If TRUE, write with readable formatting #' -#' @return NULL +#' @return NULL when file written to disk, otherwise character string #' @export #' #' @examples From c8d983b3c83c08e9541c533ddda8f2b4e303be1c Mon Sep 17 00:00:00 2001 From: "mike.stackhouse" Date: Thu, 14 Sep 2023 13:42:06 +0000 Subject: [PATCH 4/4] Associated doc updates --- man/datasetjson-package.Rd | 4 ++-- man/write_dataset_json.Rd | 3 +++ tests/testthat/_snaps/read_dataset_json.md | 7 ------- tests/testthat/_snaps/validate_dataset_json.md | 10 ---------- tests/testthat/test-read_dataset_json.R | 2 +- tests/testthat/test-validate_dataset_json.R | 2 +- 6 files changed, 7 insertions(+), 21 deletions(-) delete mode 100644 tests/testthat/_snaps/read_dataset_json.md delete mode 100644 tests/testthat/_snaps/validate_dataset_json.md diff --git a/man/datasetjson-package.Rd b/man/datasetjson-package.Rd index f85839f..fbe5b1b 100644 --- a/man/datasetjson-package.Rd +++ b/man/datasetjson-package.Rd @@ -4,9 +4,9 @@ \name{datasetjson-package} \alias{datasetjson} \alias{datasetjson-package} -\title{datasetjson: Read and write CDISC Dataset JSON files} +\title{datasetjson: Read and Write CDISC Dataset JSON Files} \description{ -R package for reading and writing CDISC Dataset JSON files. +Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) \url{https://www.cdisc.org/dataset-json}. } \seealso{ Useful links: diff --git a/man/write_dataset_json.Rd b/man/write_dataset_json.Rd index 237f06b..2945381 100644 --- a/man/write_dataset_json.Rd +++ b/man/write_dataset_json.Rd @@ -13,6 +13,9 @@ write_dataset_json(x, file, pretty = TRUE) \item{pretty}{If TRUE, write with readable formatting} } +\value{ +NULL when file written to disk, otherwise character string +} \description{ Write out a Dataset JSON file } diff --git a/tests/testthat/_snaps/read_dataset_json.md b/tests/testthat/_snaps/read_dataset_json.md deleted file mode 100644 index 917d207..0000000 --- a/tests/testthat/_snaps/read_dataset_json.md +++ /dev/null @@ -1,7 +0,0 @@ -# read_dataset_json matches xpt - - Code - e <- validate_dataset_json(test_path("testdata", "ae.json")) - Output - File contains errors! - diff --git a/tests/testthat/_snaps/validate_dataset_json.md b/tests/testthat/_snaps/validate_dataset_json.md deleted file mode 100644 index d9f06d0..0000000 --- a/tests/testthat/_snaps/validate_dataset_json.md +++ /dev/null @@ -1,10 +0,0 @@ -# validate_dataset_json returns correct messages - - Code - validate_dataset_json(js) - Output - File is valid per the Dataset JSON v1.0.0 schema - [1] instancePath schemaPath keyword params message - [6] schema parentSchema dataPath - <0 rows> (or 0-length row.names) - diff --git a/tests/testthat/test-read_dataset_json.R b/tests/testthat/test-read_dataset_json.R index f1b5640..4856c90 100644 --- a/tests/testthat/test-read_dataset_json.R +++ b/tests/testthat/test-read_dataset_json.R @@ -44,7 +44,7 @@ test_that("read_dataset_json matches xpt", { # # ae expect_error(read_dataset_json(test_path("testdata", "ae.json")), "Dataset JSON file is invalid") - expect_snapshot(e <- validate_dataset_json(test_path("testdata", "ae.json"))) + expect_warning(e <- validate_dataset_json(test_path("testdata", "ae.json")), "File contains errors!") # Simple crosscheck of the number of errors without verifying the whole dataframe expect_equal(nrow(e), 87) diff --git a/tests/testthat/test-validate_dataset_json.R b/tests/testthat/test-validate_dataset_json.R index d52e975..effad1f 100644 --- a/tests/testthat/test-validate_dataset_json.R +++ b/tests/testthat/test-validate_dataset_json.R @@ -3,6 +3,6 @@ test_that("validate_dataset_json returns correct messages", { ds_json <- dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items) js <- write_dataset_json(ds_json) - expect_snapshot(validate_dataset_json(js)) + expect_message(validate_dataset_json(js), "File is valid per the Dataset JSON v1.0.0 schema") })