diff --git a/R/column_metadata.R b/R/column_metadata.R new file mode 100644 index 0000000..cfcbb50 --- /dev/null +++ b/R/column_metadata.R @@ -0,0 +1,103 @@ +#' Verify that the item metadata supplied is the appropriate format +#' +#' This function does the following checks and consolidates to a single error message: +#' - Columns missing that must be present +#' - Columns present that are not permissible +#' - Columns with NAs that must be fully populated +#' - Columns columns that should be character or integer but aren't +#' - Within the dataType column, if the values are within the permissible list per +#' the schema +#' - Within the targetDataType column, if the values are within the permissible list per +#' the schema +#' @param items +#' +#' @return Error Check +#' @noRd +validate_dataset_columns <- function(items) { + required_cols <- c("itemOID", "name", "label", "dataType") + all_cols <- c("itemOID", "name", "label", "dataType", "targetDataType", "length", "displayFormat", "keySequence") + + # Check for missing or extraneous columns + missing_cols <- setdiff(required_cols, names(items)) + err_missing_cols <- sprintf("Column `%s` is missing and must be present", missing_cols) + additional_cols <- setdiff(names(items), all_cols) + err_additional_cols <- sprintf("Column `%s` is not a permissible column", additional_cols) + + # Check for for NAs in required columns + any_nas <- vapply(items[intersect(required_cols, names(items))], function(X) any(is.na(X)), FUN.VALUE = TRUE) + has_nas <- names(any_nas)[any_nas] + err_nas <- sprintf("Column `%s` must not have NA values", has_nas) + + # Check columns that should be character + char_cols <- intersect(c("itemOID", "name", "label", "dataType", "targetDataType", "displayFormat"), names(items)) + are_char_cols <- vapply(items[char_cols], is.character, FUN.VALUE=TRUE) + not_char_cols <- names(are_char_cols)[!are_char_cols] + err_char_cols <- sprintf("Column `%s` must be of type character", not_char_cols) + + # Check columns that should be integers + int_cols <- intersect(c("length", "keySequence"), names(items)) + are_int_cols <- vapply(items[int_cols], is.integer, FUN.VALUE=TRUE) + not_int_cols <- names(are_int_cols)[!are_int_cols] + err_int_cols <- sprintf("Column `%s` must be of type integer", not_int_cols) + + # Check that dataType values are within the permissible list + err_dataType_vars <- character() + if ('dataType' %in% names(items)) { + bad_dataType <- !(items$dataType %in% c("string", "integer", "float", "double", "decimal", "boolean", + "datetime", "date", "time", "URI")) + bad_dataType_vars <- items$name[bad_dataType] + bad_dataType_vals <- items$dataType[bad_dataType] + err_dataType_vars <- sprintf( + paste("Variable %s has an invalid dataType value of %s.", + "Must be one of string, integer, float, double, decimal, boolean, datetime, date, time, URI"), + bad_dataType_vars, bad_dataType_vals + ) + } + + # Check that targetDataType values are within the permissible list, which includes NA + # since this is optional + err_targetDataType_vars <- character() + if ('targetDataType' %in% names(items)) { + bad_targetDataType <- !(items$targetDataType %in% c("integer", "decimal", NA)) + bad_targetDataType_vars <- items$name[bad_targetDataType] + bad_targetDataType_vals <- items$targetDataType[bad_targetDataType] + err_targetDataType_vars <- sprintf( + paste("Variable %s has an invalid targetDataType value of %s.", + "Must be integer or decimal"), + bad_targetDataType_vars, bad_targetDataType_vals + ) + } + + all_errs <- c(err_missing_cols, err_additional_cols, err_nas, err_char_cols, + err_int_cols, err_dataType_vars, err_targetDataType_vars) + + if (length(all_errs) > 0) { + msg_prep <- paste0("\n\t", all_errs) + err_msg <- paste0(c("Error: Issues found in items data:", msg_prep)) + stop(err_msg, call.=FALSE) + } +} + + +set_column_metadata <- function(columns) { + # Check items before moving any further + validate_dataset_columns(columns) + + # Attach in the variable metadata + if (!("ITEMGROUPDATASEQ" %in% columns$itemOID)) { + igds_row <- data.frame( + itemOID = "ITEMGROUPDATASEQ", + name = "ITEMGROUPDATASEQ", + label = "Record Identifier", + dataType = "integer" + ) + + # Match up columns and fill + igds_row[setdiff(names(columns), names(igds_row))] <- NA + columns[setdiff(names(igds_row), names(columns))] <- NA + + columns <- rbind(igds_row, columns) + } + + columns_converted <- df_to_list_rows(columns) +} diff --git a/R/datasetjson.R b/R/datasetjson.R index ec453cc..dcace04 100644 --- a/R/datasetjson.R +++ b/R/datasetjson.R @@ -3,11 +3,11 @@ #' Create the base object used to write a Dataset JSON file. #' #' @details -#' -#' Note that DatasetJSON is on version 1.1.0. Based off findings from the pilot, -#' version 1.1.0 reflects feedback from the user community. Support for 1.0.0 has +#' +#' Note that DatasetJSON is on version 1.1.0. Based off findings from the pilot, +#' version 1.1.0 reflects feedback from the user community. Support for 1.0.0 has #' been deprecated. -#' +#' #' @param .data Input data to contain within the Dataset JSON file. Written to #' the itemData parameter. #' @param sys sourceSystem parameter, defined as "The computer system or @@ -25,9 +25,10 @@ #' @param item_oid ID used to label dataset with the itemGroupData parameter. #' Defined as "Object of Datasets. Key value is a unique identifier for #' Dataset, corresponding to ItemGroupDef/@OID in Define-XML." -#' @param ref_data Boolean value that is set to "true" when the dataset contains -#' reference data (not subject data). The default value is "false". +#' @param ref_data Boolean value that is set to "true" when the dataset contains +#' reference data (not subject data). The default value is "false". #' @param version The DatasetJSON version to use. Currently only 1.1.0 is supported. +#' @param columns Variable level metadata for the Dataset JSON object #' #' @return dataset_json object pertaining to the specific Dataset JSON version #' specific @@ -36,18 +37,19 @@ #' @examples #' # Create a basic object #' ds_json <- dataset_json( -#' iris, +#' iris, #' file_oid = "/some/path", #' last_modified = "2023-02-15T10:23:15", -#' originator = "Some Org", -#' sys = "source system", -#' sys_version = "1.0", +#' originator = "Some Org", +#' sys = "source system", +#' sys_version = "1.0", #' study = "SOMESTUDY", #' metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", #' metadata_ref = "some/define.xml", #' item_oid = "IG.IRIS", #' name = "IRIS", -#' dataset_label = "Iris" +#' dataset_label = "Iris", +#' columns = iris_items #' ) #' #' # Attach attributes directly @@ -62,14 +64,15 @@ #' ds_json_updated <- set_item_oid(ds_json_updated, "IG.IRIS") #' ds_json_updated <- set_dataset_name(ds_json_updated, "IRIS") #' ds_json_updated <- set_dataset_label(ds_json_updated, "Iris") -dataset_json <- function(.data, file_oid = NULL, last_modified=NULL, - originator=NULL, sys=NULL, sys_version = NULL, - study=NULL, metadata_version=NULL,metadata_ref=NULL, - item_oid=NULL, name=NULL, dataset_label=NULL, ref_data=FALSE, - version="1.1.0") { - new_dataset_json(.data, file_oid, last_modified, originator, sys, sys_version, study, - metadata_version, metadata_ref, item_oid, name, dataset_label, ref_data, - version) +#' ds_json_updates <- set_columns(ds_json_updated, iris_items) +dataset_json <- function(.data, file_oid=NULL, last_modified=NULL, + originator=NULL, sys=NULL, sys_version = NULL, + study=NULL, metadata_version=NULL,metadata_ref=NULL, + item_oid=NULL, name=NULL, dataset_label=NULL, ref_data=FALSE, + columns=NULL, version="1.1.0") { + new_dataset_json(.data, file_oid, last_modified, originator, sys, sys_version, study, + metadata_version, metadata_ref, item_oid, name, dataset_label, ref_data, + columns, version) } #' Create a base Dataset JSON Container @@ -81,9 +84,9 @@ dataset_json <- function(.data, file_oid = NULL, last_modified=NULL, #' @return datasetjson object #' #' @noRd -new_dataset_json <- function(.data, file_oid, last_modified, originator, sys, sys_version, study, +new_dataset_json <- function(.data, file_oid, last_modified, originator, sys, sys_version, study, metadata_version, metadata_ref, item_oid, name, dataset_label, - ref_data, version) { + ref_data, columns, version) { if (!(version %in% c("1.1.0"))) { stop("Unsupported version specified - currently only version 1.1.0 is supported", call.=FALSE) @@ -95,18 +98,18 @@ new_dataset_json <- function(.data, file_oid, last_modified, originator, sys, sy ) # Extract the function and call it to return the base structure - funcs[[version]](.data, file_oid, last_modified, originator, sys, sys_version, study, + funcs[[version]](.data, file_oid, last_modified, originator, sys, sys_version, study, metadata_version, metadata_ref, item_oid, name, dataset_label, - ref_data) + ref_data, columns) } #' Dataset JSON v1.1.0 Generator #' #' @return datasetjson_v1_1_0 object #' @noRd -new_dataset_json_v1_1_0 <- function(.data, file_oid, last_modified, originator, sys, sys_version, - study, metadata_version, metadata_ref, item_oid, name, - dataset_label, ref_data) { +new_dataset_json_v1_1_0 <- function(.data, file_oid, last_modified, originator, sys, sys_version, + study, metadata_version, metadata_ref, item_oid, name, + dataset_label, ref_data, columns) { if (!inherits(.data, 'data.frame')) { stop("datasetjson objects must inherit from a data.frame", call.=FALSE) @@ -130,7 +133,11 @@ new_dataset_json_v1_1_0 <- function(.data, file_oid, last_modified, originator, attr(.data, 'name') <- name attr(.data, 'label') <- dataset_label attr(.data, 'isReferenceData') <- ref_data - + if (!is.null(columns)) { + validate_dataset_columns(columns) + } + attr(.data, 'columns') <- set_column_metadata(columns) + structure( .data, class = c("datasetjson_v1_1_0", "datasetjson", "data.frame") diff --git a/R/read_dataset_json.R b/R/read_dataset_json.R index a389558..8486cbf 100644 --- a/R/read_dataset_json.R +++ b/R/read_dataset_json.R @@ -48,19 +48,16 @@ read_dataset_json <- function(file) { ) } - - - # Pull the object out with a lot of assumptions because the format has already - # been validated - dtype <- ifelse("clinicalData" %in% names(ds_json), "clinicalData", "referenceData") - d <- as.data.frame(ds_json[[dtype]]$itemGroupData[[1]]$itemData) - items <- ds_json[[dtype]]$itemGroupData[[1]]$items + # Pull the data and items + d <- as.data.frame(ds_json$rows) + items <- ds_json$columns # Start setting attributes colnames(d) <- items$name # Process type conversions - tt <- items$type + tt <- items$dataType + tdt <- items$targetDataType int_cols <- tt == "integer" dbl_cols <- tt %in% c("float", "double", "decimal") bool_cols <- tt == "boolean" @@ -68,39 +65,40 @@ read_dataset_json <- function(file) { d[dbl_cols] <- lapply(d[dbl_cols], as.double) d[bool_cols] <- lapply(d[bool_cols], as.logical) - # Grab date and datetime column info - fmts <- items$displayFormat - date_cols <- fmts %in% sas_date_formats - datetime_cols <- fmts %in% sas_datetime_formats - d[date_cols] <- lapply(d[date_cols], as.Date, origin="1960-01-01") - d[datetime_cols] <- lapply(d[datetime_cols], as.POSIXct, origin="1960-01-01") + date_cols <- tt %in% c("date") & tdt %in% "integer" + datetime_cols <- tt %in% c("datetime", "time") & tdt %in% "integer" + d[date_cols] <- lapply(d[date_cols], as.Date) + d[datetime_cols] <- lapply(d[datetime_cols], as.POSIXct) # Apply variable labels d[names(d)] <- lapply(items$name, set_col_attr, d, 'label', items) - d[names(d)] <- lapply(items$name, set_col_attr, d, 'OID', items) - d[names(d)] <- lapply(items$name, set_col_attr, d, 'length', items) - d[names(d)] <- lapply(items$name, set_col_attr, d, 'type', items) - d[names(d)] <- lapply(items$name, set_col_attr, d, 'keySequence', items) - d[names(d)] <- lapply(items$name, set_col_attr, d, 'displayFormat', items) d <- d[,-1] # get rid of ITEMGROUPDATASEQ column - # Apply file and data level attributes - attr(d, 'creationDateTime') <- ds_json$creationDateTime - attr(d, 'datasetJSONVersion') <- ds_json$datasetJSONVersion - attr(d, 'fileOID') <- ds_json$fileOID - attr(d, 'asOfDateTime') <- ds_json$asOfDateTime - attr(d, 'originator') <- ds_json$originator - attr(d, 'sourceSystem') <- ds_json$sourceSystem - attr(d, 'sourceSystemVersion') <- ds_json$sourceSystemVersion - attr(d, 'name') <-ds_json[[dtype]]$itemGroupData[[1]]$name - attr(d, 'records') <-ds_json[[dtype]]$itemGroupData[[1]]$records - attr(d, 'label') <-ds_json[[dtype]]$itemGroupData[[1]]$label + ds_attr <- dataset_json( + d, + file_oid = ds_json$fileOID, + originator = ds_json$originator, + sys = ds_json$sourceSystem$name, + sys_version = ds_json$sourceSystem$version, + study = ds_json$studyOID, + metadata_version = ds_json$metaDataVersionOID, + metadata_ref = ds_json$metaDataRef, + item_oid = ds_json$itemGroupOID, + name = ds_json$name, + dataset_label = ds_json$label, + ref_data = ds_json$isReferenceData, + last_modified = ds_json$dbLastModifiedDateTime, + version = ds_json$datasetJSONVersion, + columns = ds_json$columns + ) + + # Apply records and column attribute + if(ds_json$records != nrow(d)) { + warning("The number of rows in the data does not match the number of records recorded in the metadata.") + } - # Still save the name of the element storing the dataset metadata - ds_json[[dtype]]$itemGroupData <- names(ds_json[[dtype]]$itemGroupData) + attr(ds_attr, 'records') <- ds_json$records - # Store the data metadata still within it's own list - attr(d, dtype) <- ds_json[[dtype]] - d + ds_attr } diff --git a/R/utils.R b/R/utils.R index 650ed21..bbb0694 100644 --- a/R/utils.R +++ b/R/utils.R @@ -10,35 +10,6 @@ stopifnot_datasetjson <- function(x) { } } -stopifnot_dataset_metadata <- function(x) { - if (!(inherits(x, "datasetjson") | inherits(x, "dataset_metadata"))) { - stop("Input must be a datasetjson or dataset_metadata object", call.=FALSE) - } -} - -stopifnot_data_metadata <- function(x) { - if (!(inherits(x, "datasetjson") | inherits(x, "data_metadata"))) { - stop("Input must be a datasetjson or data_metadata object", call.=FALSE) - } -} - -stopifnot_file_metadata <- function(x) { - if (!(inherits(x, "datasetjson") | inherits(x, "file_metadata"))) { - stop("Input must be a datasetjson object or file_metadata object", call.=FALSE) - } -} - -#' Retrieve the data type of a datasetjson object -#' -#' @param x A datasetjson object -#' -#' @return A character string containing the Datset JSON data type -#' @noRd -get_data_type <- function(x) { - stopifnot_datasetjson(x) - tail(names(x), 1) -} - #' Helper to set column attributes from items metadata #' #' @param nm Column name @@ -65,30 +36,7 @@ get_null_inds <- function(x) { which(vapply(x, is.null, FUN.VALUE = TRUE)) } -#' Remove nulls from a Dataset JSON object -#' -#' Only targets the file and data metadata to pull off optional elements -#' -#' @param x A Dataset JSON object -#' -#' @return A Dataset JSON object -#' @noRd -remove_nulls <- function(x) { - - # Specifically target the data metadata - dm_nulls <- get_null_inds(x[[get_data_type(x)]]) - if (length(dm_nulls) > 0) { - x[[get_data_type(x)]] <- x[[get_data_type(x)]][-dm_nulls] - } - # Top level - fm_nulls <- get_null_inds(x) - if (length(fm_nulls) > 0) { - x <- x[-fm_nulls] - } - - x -} #' Check if given path is a URL #' @@ -115,3 +63,24 @@ read_from_url <- function(path) { close(con) x } + +#' Convert an dataframe into a named list of rows without NAs +#' +#' The variable attributes are stored as named lists within the output +#' JSON file, so to write them out the dataframe needs to be a named +#' list of rows +#' +#' @param x A data.frame +#' +#' @return List of named lists with single elements +#' @noRd +df_to_list_rows <- function(x) { + # Split the dataframe rows into individual rows + rows <- unname(split(x, seq(nrow(x)))) + # Convert each row into a named list while removing NAs + lapply(rows, function(X) { + y <- as.list(X) + y[!is.na(y)] + }) +} + diff --git a/R/write_dataset_json.R b/R/write_dataset_json.R index 099bba0..20dc0b9 100644 --- a/R/write_dataset_json.R +++ b/R/write_dataset_json.R @@ -10,7 +10,7 @@ #' @examples #' # Write to character object #' ds_json <- dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items) -#' js <- write_dataset_json(ds_json) +#' js <- write_dataset_json(ds_json, iris_items) #' #' # Write to disk #' \dontrun{ @@ -20,9 +20,36 @@ write_dataset_json <- function(x, file, pretty=FALSE) { stopifnot_datasetjson(x) # Populate the creation datetime - x[['creationDateTime']] <- get_datetime() + attr(x, 'datasetJSONCreationDateTime') <- get_datetime() - x <- remove_nulls(x) + # Store number of records + records <- nrow(x) + attr(x, 'records') <- records + + # Pull attributes into a list and order + temp <- attributes(x)[c( + "datasetJSONCreationDateTime", + "datasetJSONVersion", + "fileOID", + "dbLastModifiedDateTime", + "originator", + "sourceSystem", + "studyOID", + "metaDataVersionOID", + "metaDataRef", + "itemGroupOID", + "isReferenceData", + "records", + "name", + "label", + "columns") + ] + + # add ITEMGROUPDATASEQ to data + x <- cbind(ITEMGROUPDATASEQ = 1:records, x) + + # add data rows + temp$rows <- unname(x) if (!missing(file)) { # Make sure the output path exists @@ -40,14 +67,14 @@ write_dataset_json <- function(x, file, pretty=FALSE) { if (!missing(file)) { # Write file to disk yyjsonr::write_json_file( - x, + temp, filename = file, opts = json_opts ) } else { # Print to console yyjsonr::write_json_str( - x, + temp, opts = json_opts ) } diff --git a/data/iris_items.rda b/data/iris_items.rda index c817b7b..d5b350f 100644 Binary files a/data/iris_items.rda and b/data/iris_items.rda differ diff --git a/tests/testthat/_snaps/dataset_metadata.md b/tests/testthat/_snaps/dataset_metadata.md deleted file mode 100644 index ba7b48e..0000000 --- a/tests/testthat/_snaps/dataset_metadata.md +++ /dev/null @@ -1,11 +0,0 @@ -# items validator generates messages as expected - - Error: Issues found in items data: - Column `label` is missing and must be present - Column `bad_col` is not a permissible column - Column `OID` must not have NA values - Column `name` must be of type character - Column `keySequence` must be of type integer - Variable 1 has an invalid type value of numeric. Must be one of string, integer, float, double, decimal, boolean - Variable 5 has an invalid type value of character. Must be one of string, integer, float, double, decimal, boolean - diff --git a/tests/testthat/test-data_metadata.R b/tests/testthat/test-data_metadata.R deleted file mode 100644 index 6a6cce9..0000000 --- a/tests/testthat/test-data_metadata.R +++ /dev/null @@ -1,17 +0,0 @@ -data_meta <- data_metadata() - -test_that("Default data_metadata object produces correctly", { - expect_null(data_meta$studyOID) - expect_null(data_meta$metaDataVersionOID) - expect_null(data_meta$metaDataRef) -}) - -test_that("data_metadata setters work properly", { - data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml") - data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7") - data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY") - - expect_equal(data_meta_updated$studyOID, "SOMESTUDY") - expect_equal(data_meta_updated$metaDataVersionOID, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7") - expect_equal(data_meta_updated$metaDataRef, "some/define.xml") -}) diff --git a/tests/testthat/test-dataset_metadata.R b/tests/testthat/test-dataset_metadata.R deleted file mode 100644 index 1e834af..0000000 --- a/tests/testthat/test-dataset_metadata.R +++ /dev/null @@ -1,64 +0,0 @@ -iris_items_bad <- readRDS(test_path("testdata", "iris_items_bad.Rds")) -iris_items_list <- readRDS(test_path("testdata", "iris_items_list.Rds")) - -iris_items_test <- rbind( - data.frame(OID = "ITEMGROUPDATASEQ", - name = "ITEMGROUPDATASEQ", - label = "Record Identifier", - type = "integer", - length = NA_integer_, - keySequence = NA_integer_, - displayFormat = NA_character_), - iris_items -) - -test_that("Basic call produces expected object", { - dataset_meta <- dataset_metadata( - item_id = "IG.IRIS", - name = "IRIS", - label = "Iris", - items = iris_items - ) - - expect_null(dataset_meta$IG.IRIS$records) - expect_equal(dataset_meta$IG.IRIS$name, "IRIS") - expect_equal(dataset_meta$IG.IRIS$label, "Iris") - - # Verify that ITEMGROUPSEQ is attached properly - expect_equal(dataset_meta$IG.IRIS$items, iris_items_list) - - expect_null(dataset_meta$IG.IRIS$itemData) -}) - -test_that("ITEMGROUPDATASEQ will not duplicate when provided and data attaches properly", { - dataset_meta <- dataset_metadata( - item_id = "IG.IRIS", - name = "IRIS", - label = "Iris", - items = iris_items_test, - .data = iris - ) - - expect_equal(dataset_meta$IG.IRIS$items, iris_items_list) -}) - -test_that("items validator generates messages as expected", { - expect_snapshot_error(dataset_metadata( - item_id = "IG.IRIS", - name = "IRIS", - label = "Iris", - items = iris_items_bad - )) -}) - -test_that("dataset_metadata generates messages as expected", { - expect_error( - dataset_metadata( - item_id = "IG.IRIS", - name = "IRIS", - label = "Iris", - items = iris_items_test, - .data = as.matrix(iris) - ), ".data must be a data.frame" - ) -}) diff --git a/tests/testthat/test-datasetjson.R b/tests/testthat/test-datasetjson.R index 52576a0..91be1eb 100644 --- a/tests/testthat/test-datasetjson.R +++ b/tests/testthat/test-datasetjson.R @@ -1,5 +1,22 @@ # Objects to use for testing -ds_json <- dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items) +iris_metadata <- readRDS(test_path("testdata", "iris_metadata.Rds")) + +ds_json <- dataset_json( + iris, + # file_oid = "/some/path", + # last_modified = "2023-02-15T10:23:15", + # originator = "Some Org", + # sys = "source system", + # sys_version = "1.0", + # study = "SOMESTUDY", + # metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", + # metadata_ref = "some/define.xml", + item_oid = "IG.IRIS", + name = "IRIS", + dataset_label = "Iris", + columns = iris_metadata +) + iris_items_list <- readRDS(test_path("testdata", "iris_items_list.Rds")) # This test will verify that everything lands where expected and auto-calculated @@ -10,126 +27,49 @@ test_that("datasetjson object builds with minimal defaults", { # where the call to system time splits across a second # expect_equal(grep("\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}", ds_json$creationDateTime), 1) - # File metadata - expect_equal(ds_json$datasetJSONVersion, "1.0.0") - expect_null(ds_json$fileOID) - expect_null(ds_json$asOfDateTime) - expect_null(ds_json$originator) - expect_null(ds_json$sourceSystem) - expect_null(ds_json$sourceSystemVersion) - - # Data type is correct - expect_equal(tail(names(ds_json), 1), "clinicalData") - - # Data metadata - expect_null(ds_json$clinicalData$studyOID) - expect_null(ds_json$clinicalData$metaDataVersionOID) - expect_null(ds_json$clinicalData$metaDataRef) - - # item_id passes through - expect_equal(names(ds_json$clinicalData$itemGroupData), "IG.IRIS") - - # Dataset metadata - expect_equal(ds_json$clinicalData$itemGroupData$IG.IRIS$records, nrow(iris)) - expect_equal(ds_json$clinicalData$itemGroupData$IG.IRIS$name, "IRIS") - expect_equal(ds_json$clinicalData$itemGroupData$IG.IRIS$label, "Iris") - - # Verify that ITEMGROUPSEQ is attached properly - iris_items_test <- rbind( - data.frame(OID = "ITEMGROUPDATASEQ", - name = "ITEMGROUPDATASEQ", - label = "Record Identifier", - type = "integer", - length = NA_integer_, - keySequence = NA_integer_, - displayFormat = NA_character_), - iris_items - ) + # Metadata + expect_null(attr(ds_json, "datasetJSONCreationDateTime")) + expect_equal(attr(ds_json, "datasetJSONVersion"), "1.1.0") + expect_null(attr(ds_json, "fileOID")) + expect_null(attr(ds_json, "dbLastModifiedDateTime")) + expect_null(attr(ds_json, "originator")) + expect_null(attr(ds_json, "sourceSystem")) + expect_null(attr(ds_json, "studyOID")) + expect_null(attr(ds_json, "metaDataVersionOID")) + expect_null(attr(ds_json, "metaDataRef")) + expect_equal(attr(ds_json, "itemGroupOID"), "IG.IRIS") + expect_equal(attr(ds_json, "isReferenceData"), FALSE) + expect_null(attr(ds_json, "records")) + expect_equal(attr(ds_json, "name"), "IRIS") + expect_equal(attr(ds_json, "label"), "Iris") + expect_equal(attr(ds_json, "columns"), iris_items_list) - expect_equal(ds_json$clinicalData$itemGroupData$IG.IRIS$items, iris_items_list) - - # Verify that data are attached properly with ITEMGRPUPSEQ attached - iris_test <- unname(cbind( - ITEMGROUPDATASEQ = 1:nrow(iris), - iris - )) - - expect_equal(ds_json$clinicalData$itemGroupData$IG.IRIS$itemData, iris_test) }) test_that("datasetjson setter functions insert info in the right fields", { - ds_json_updated <- set_data_type(ds_json, "referenceData") - ds_json_updated <- set_file_oid(ds_json_updated, "/some/path") + ds_json_updated <- set_file_oid(ds_json, "/some/path") ds_json_updated <- set_metadata_ref(ds_json_updated, "some/define.xml") ds_json_updated <- set_metadata_version(ds_json_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7") ds_json_updated <- set_originator(ds_json_updated, "Some Org") ds_json_updated <- set_source_system(ds_json_updated, "source system", "1.0") ds_json_updated <- set_study_oid(ds_json_updated, "SOMESTUDY") - expect_equal(tail(names(ds_json_updated), 1), "referenceData") - expect_equal(ds_json_updated$fileOID, "/some/path") - expect_equal(ds_json_updated$originator, "Some Org") - expect_equal(ds_json_updated$sourceSystem, "source system") - expect_equal(ds_json_updated$sourceSystemVersion, "1.0") - expect_equal(ds_json_updated$referenceData$studyOID, "SOMESTUDY") - expect_equal(ds_json_updated$referenceData$metaDataVersionOID, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7") - expect_equal(ds_json_updated$referenceData$metaDataRef, "some/define.xml") -}) - -test_that("Data type passes through", { - x <- dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items, data_type = "referenceData") - expect_equal(tail(names(x), 1), "referenceData") + expect_equal(attr(ds_json_updated, "fileOID"), "/some/path") + expect_equal(attr(ds_json_updated, "originator"), "Some Org") + expect_equal(attr(ds_json_updated, "sourceSystem"), list(name = "source system", version = "1.0")) + expect_equal(attr(ds_json_updated, "studyOID"), "SOMESTUDY") + expect_equal(attr(ds_json_updated, "metaDataVersionOID"), "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7") + expect_equal(attr(ds_json_updated, "metaDataRef"), "some/define.xml") }) # Error checking test_that("Errors are thrown properly", { expect_error( - dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items, data_type = "blah"), - regexp = "should be one of" - ) - - expect_error( - dataset_json(iris, item_id = "IG.IRIS", name = "IRIS", items = iris_items), - "If dataset_meta is not provided, then name, label, and items must be provided" - ) - - expect_error( - dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items, version="2"), + dataset_json(iris, version="2"), regexp = "Unsupported version specified" ) -}) - -test_that("Object builds from prespecified metadata objects", { - file_meta <- file_metadata( - originator = "Some Org", - sys = "source system", - sys_version = "1.0" - ) - - data_meta <- data_metadata( - study = "SOMESTUDY", - metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", - metadata_ref = "some/define.xml" - ) - - dataset_meta <- dataset_metadata( - item_id = "IG.IRIS", - name = "IRIS", - label = "Iris", - items = iris_items + expect_error( + dataset_json(as.list(iris), version="1.1.0"), + regexp = "must inherit from a data.frame" ) - - ds_json_from_meta <- dataset_json(iris, - dataset_meta = dataset_meta, - file_meta = file_meta, - data_meta = data_meta) - - - expect_equal(tail(names(ds_json_from_meta), 1), "clinicalData") - expect_equal(ds_json_from_meta$originator, "Some Org") - expect_equal(ds_json_from_meta$sourceSystem, "source system") - expect_equal(ds_json_from_meta$sourceSystemVersion, "1.0") - expect_equal(ds_json_from_meta$clinicalData$studyOID, "SOMESTUDY") - expect_equal(ds_json_from_meta$clinicalData$metaDataVersionOID, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7") - expect_equal(ds_json_from_meta$clinicalData$metaDataRef, "some/define.xml") }) diff --git a/tests/testthat/test-date_time_conversions.R b/tests/testthat/test-date_time_conversions.R deleted file mode 100644 index 56e90e0..0000000 --- a/tests/testthat/test-date_time_conversions.R +++ /dev/null @@ -1,20 +0,0 @@ -test_df <- data.frame( - d1 = as.Date(c(19906:19916), origin="1960-01-01") + (365 * 10), - d2 = as.Date(c(19916:19926), origin="1960-01-01") + (365 * 10), - dt1 = as.POSIXct(((19906:19916) + (365 * 10)) * 24 * 60 * 60 + (2 * 60 * 60) + (45 * 60) + 20, origin="1960-01-01"), - dt2 = as.POSIXct(((19916:19926) + (365 * 10)) * 24 * 60 * 60 + (2 * 60 * 60) + (45 * 60) + 20, origin="1960-01-01") -) - -check_df <- test_df -check_df[1:2] <- check_df[1:2] + (365 * 10 + 3) -check_df[3:4] <- check_df[3:4] + ((365 * 10 + 3) * 24 * 60 * 60) - -test_that("Check that columns convert as expected", { - x <- test_df - x <- convert_to_sas_datenum(x) - x <- convert_to_sas_datetimenum(x) - x[1:2] <- lapply(x[1:2], as.Date, origin="1970-01-01") - x[3:4] <- lapply(x[3:4], as.POSIXct, origin="1970-01-01") - - expect_equal(x, check_df, ignore_attr=TRUE) -}) diff --git a/tests/testthat/test-file_metadata.R b/tests/testthat/test-file_metadata.R deleted file mode 100644 index 5da222a..0000000 --- a/tests/testthat/test-file_metadata.R +++ /dev/null @@ -1,48 +0,0 @@ -test_that("Default file_metadata object produces correctly", { - file_meta <- file_metadata() - - expect_equal(file_meta$datasetJSONVersion, "1.0.0") - expect_null(file_meta$fileOID, character()) - expect_null(file_meta$asOfDateTime) - expect_null(file_meta$originator) - expect_null(file_meta$sourceSystem) - expect_null(file_meta$sourceSystemVersion) -}) - -test_that("Parameters pass through on file_metadata call", { - file_meta <- file_metadata( - originator = "Some Org", - sys = "source system", - sys_version = "1.0" - ) - - expect_equal(file_meta$originator, "Some Org") - expect_equal(file_meta$sourceSystem, "source system") - expect_equal(file_meta$sourceSystemVersion, "1.0") -}) - -test_that("get_datetime() produces properly formatted datetime", { - expect_equal(grep("\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}", get_datetime()), 1) -}) - -test_that("Setters work on file_metadata objects", { - - file_meta <- file_metadata() - - file_meta_updated <- set_file_oid(file_meta, "/some/path") - file_meta_updated <- set_originator(file_meta_updated, "Some Org") - file_meta_updated <- set_source_system(file_meta_updated, "source system", "1.0") - - expect_equal(file_meta_updated$fileOID, "/some/path") - expect_equal(file_meta_updated$originator, "Some Org") - expect_equal(file_meta_updated$sourceSystem, "source system") - expect_equal(file_meta_updated$sourceSystemVersion, "1.0") -}) - -# Error checking -test_that("Errors are thrown properly", { - expect_error( - file_metadata(version = "2.0.0"), - "Unsupported version specified - currently only version 1.0.0 is supported" - ) -}) diff --git a/tests/testthat/test-read_dataset_json.R b/tests/testthat/test-read_dataset_json.R index 802a8fa..c24428b 100644 --- a/tests/testthat/test-read_dataset_json.R +++ b/tests/testthat/test-read_dataset_json.R @@ -1,52 +1,49 @@ test_that("read_dataset_json matches xpt", { - # adsl + # adsl ---- df_name <- "adsl" comp <- read_dataset_json(test_path(paste0("testdata/", df_name, ".json"))) expected <- haven::read_xpt(test_path(paste0("testdata/", df_name, ".xpt"))) expect_equal(comp, expected, ignore_attr = TRUE) - # adsl attributes check + # adsl attributes check for those available in xpt comp_attr <- attributes(comp) comp_expected <- attributes(expected) - expect_equal(comp_attr[["names"]], comp_expected[["names"]]) expect_equal(comp_attr[["row.names"]], comp_expected[["row.names"]]) expect_equal(comp_attr[["label"]], comp_expected[["label"]]) + expect_equal(comp_attr[["names"]], comp_expected[["names"]]) + - # ta + # ta ---- df_name <- "ta" comp <- read_dataset_json(test_path(paste0("testdata/", df_name, ".json"))) expected <- haven::read_xpt(test_path(paste0("testdata/", df_name, ".xpt"))) expect_equal(comp, expected, ignore_attr = TRUE) - # ta attributes check + # ta attributes check for those available in xpt comp_attr <- attributes(comp) comp_expected <- attributes(expected) - expect_equal(comp_attr[["names"]], comp_expected[["names"]]) expect_equal(comp_attr[["row.names"]], comp_expected[["row.names"]]) expect_equal(comp_attr[["label"]], comp_expected[["label"]]) + expect_equal(comp_attr[["names"]], comp_expected[["names"]]) - # dm + # dm ---- df_name <- "dm" comp <- read_dataset_json(test_path(paste0("testdata/", df_name, ".json"))) expected <- haven::read_xpt(test_path(paste0("testdata/", df_name, ".xpt"))) expect_equal(comp, expected, ignore_attr = TRUE) - # dm attributes check + # dm attributes check for those available in xpt comp_attr <- attributes(comp) comp_expected <- attributes(expected) - expect_equal(comp_attr[["names"]], comp_expected[["names"]]) - expect_equal(comp_attr[["row.names"]], comp_expected[["row.names"]]) - expect_equal(comp_attr[["label"]], comp_expected[["label"]]) - - # # ae - expect_warning(e <- validate_dataset_json(test_path("testdata", "ae.json")), "File contains errors!") + # invalid json ---- + expect_warning(e <- validate_dataset_json(test_path("testdata", "invalid_dm.json")), "File contains errors!") # Simple crosscheck of the number of errors without verifying the whole dataframe - expect_equal(nrow(e), 87) + expect_equal(nrow(e), 1) }) @@ -61,7 +58,21 @@ test_that("Dataset JSON can be read from a URL", { }) test_that("Dataset JSON can be read from imported string", { - ds_json <- dataset_json(iris[1:5, ], "IG.IRIS", "IRIS", "Iris", iris_items) + ds_json <- dataset_json( + iris[1:5, ], + file_oid = "/some/path", + last_modified = "2023-02-15T10:23:15", + originator = "Some Org", + sys = "source system", + sys_version = "1.0", + study = "SOMESTUDY", + metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", + metadata_ref = "some/define.xml", + item_oid = "IG.IRIS", + name = "IRIS", + dataset_label = "Iris", + columns = iris_items + ) js <- write_dataset_json(ds_json, pretty=TRUE) expect_silent(dat <- read_dataset_json(js)) x <- iris diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R index 562d370..7931f67 100644 --- a/tests/testthat/test-utils.R +++ b/tests/testthat/test-utils.R @@ -1,43 +1,13 @@ test_that("Type checker functions throw proper errors", { - expect_error(set_data_type(1), "Input must be a datasetjson object") + expect_error(set_source_system(1, "sys", "ver"), "Input must be a datasetjson object") + expect_error(set_originator(1, "orig"), "Input must be a datasetjson object") + expect_error(set_file_oid(1, "path"), "Input must be a datasetjson object") - expect_error(set_source_system(1, "sys", "ver"), "Input must be a datasetjson object or file_metadata object") - expect_error(set_originator(1, "orig"), "Input must be a datasetjson object or file_metadata object") - expect_error(set_file_oid(1, "path"), "Input must be a datasetjson object or file_metadata object") - - expect_error(set_study_oid(1, "study"), "Input must be a datasetjson or data_metadata object") - expect_error(set_metadata_version(1, "study"), "Input must be a datasetjson or data_metadata object") - expect_error(set_metadata_ref(1, "ref"), "Input must be a datasetjson or data_metadata object") - - expect_error(set_item_data(1, iris), "Input must be a datasetjson or dataset_metadata object") + expect_error(set_study_oid(1, "study"), "Input must be a datasetjson") + expect_error(set_metadata_version(1, "study"), "Input must be a datasetjson") + expect_error(set_metadata_ref(1, "ref"), "Input must be a datasetjson") }) -test_that("NULL removals process effectively", { - ds_json <- dataset_json(iris[1, ], "IG.IRIS", "IRIS", "Iris", iris_items) - - x <- remove_nulls(ds_json) - - non_null_names_fm <- c( - "creationDateTime", "datasetJSONVersion", "fileOID", "asOfDateTime", "originator", - "sourceSystem", "sourceSystemVersion", "clinicalData" - ) - - non_null_names_dm <- c( - "studyOID", "metaDataVersionOID", "metaDataRef", "itemGroupData" - ) - - expect_equal(names(ds_json), non_null_names_fm) - expect_equal(names(ds_json$clinicalData), non_null_names_dm) - - null_names_fm <- c( - "creationDateTime", "datasetJSONVersion", "clinicalData" - ) - - null_names_dm <- "itemGroupData" - - expect_equal(names(x), null_names_fm) - expect_equal(names(x$clinicalData), null_names_dm) -}) test_that("URL checker regex works as expected", { url_list <- c( diff --git a/tests/testthat/test-validate_dataset_json.R b/tests/testthat/test-validate_dataset_json.R index 94f821f..4e7c610 100644 --- a/tests/testthat/test-validate_dataset_json.R +++ b/tests/testthat/test-validate_dataset_json.R @@ -1,19 +1,33 @@ test_that("validate_dataset_json returns correct messages", { - ds_json <- dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items) + ds_json <- dataset_json( + iris, + file_oid = "/some/path", + last_modified = "2023-02-15T10:23:15", + originator = "Some Org", + sys = "source system", + sys_version = "1.0", + study = "SOMESTUDY", + metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", + metadata_ref = "some/define.xml", + item_oid = "IG.IRIS", + name = "IRIS", + dataset_label = "Iris", + columns = iris_items + ) js <- write_dataset_json(ds_json) - expect_message(validate_dataset_json(js), "File is valid per the Dataset JSON v1.0.0 schema") + expect_message(validate_dataset_json(js), "File is valid per the Dataset JSON v1.1.0 schema") }) test_that("JSON can checked from URL", { - fpath <- paste0("file://", normalizePath(test_path("testdata", "ae.json"))) + fpath <- paste0("file://", normalizePath(test_path("testdata", "invalid_dm.json"))) expect_warning( err <- validate_dataset_json(fpath), "File contains errors!" ) # Loose check of number of issues - expect_equal(dim(err), c(87, 9)) + expect_equal(dim(err), c(1, 9)) }) diff --git a/tests/testthat/test-write_dataset_json.R b/tests/testthat/test-write_dataset_json.R index 0603b28..8063660 100644 --- a/tests/testthat/test-write_dataset_json.R +++ b/tests/testthat/test-write_dataset_json.R @@ -1,30 +1,27 @@ -set_test_adam_metadata <- function(ds_json){ - ds_json <- set_originator(ds_json, "CDISC ADaM MSG Team") - ds_json <- set_source_system(ds_json, "Sponsor System", "1.0") - ds_json <- set_metadata_ref(ds_json, "https://metadata.location.org/TDF_ADaM_ADaMIG11/define.xml") - ds_json <- set_metadata_version(ds_json, "MDV.TDF_ADaM.ADaMIG.1.1") - ds_json <- set_study_oid(ds_json, "TDF_ADaM.ADaMIG.1.1") - ds_json -} -set_test_sdtm_metadata <- function(ds_json){ - ds_json <- set_originator(ds_json, "CDISC SDTM MSG Team") - ds_json <- set_source_system(ds_json, "Sponsor System", "1.0") - ds_json <- set_metadata_ref(ds_json, "https://metadata.location.org/CDISCPILOT01/define.xml") - ds_json <- set_metadata_version(ds_json, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7") - ds_json <- set_study_oid(ds_json, "cdisc.com/CDISCPILOT01") - ds_json -} test_that("write_dataset_json matches the original json", { # adsl df_name <- "adsl" - df_from_json <- read_dataset_json(test_path(paste0("testdata/", df_name, ".json"))) + orig_df <- haven::read_xpt(test_path(paste0("testdata/", df_name, ".xpt"))) df_metadata <- readRDS(test_path("testdata/adsl_metadata.Rds")) # create dataset json object - ds_json <- dataset_json(df_from_json, "IG.ADSL", "ADSL", "Subject-Level Analysis Dataset", df_metadata) - ds_json <- set_test_adam_metadata(ds_json) + ds_json <- dataset_json( + orig_df, + file_oid = "www.cdisc.org/StudyMSGv1/1/Define-XML_2.1.0/2024-08-05/adsl", + last_modified = "2024-08-05T10:08:46", + originator = "CDISC ADaM MSG Team", + sys = "SAS on X64_10PRO", + sys_version = "9.0401M7", + study = "TDF_ADaM.ADaMIG.1.1", + metadata_version = "MDV.TDF_ADaM.ADaMIG.1.1", + metadata_ref = "define.xml", + item_oid = "IG.ADSL", + name = "ADSL", + dataset_label = "Subject-Level Analysis Dataset", + columns = df_metadata + ) # write json to disk json_location <- paste0(df_name,".json") @@ -34,25 +31,34 @@ test_that("write_dataset_json matches the original json", { comp <- jsonlite::read_json(json_location) expected <- jsonlite::read_json(test_path("testdata/adsl.json")) - # remove fileOID and creationDateTime, this will always differ - # remove asOfDateTime, this is not in adsl.json (to confirm if extensible) - comp$fileOID <- NULL - expected$fileOID <- NULL - comp$asOfDateTime <- NULL - comp$creationDateTime <- NULL - expected$creationDateTime <- NULL + # remove datasetJSONCreationDateTime, this will always differ + comp$datasetJSONCreationDateTime <- NULL + expected$datasetJSONCreationDateTime <- NULL expect_equal(comp, expected) # dm df_name <- "dm" - df_from_json <- read_dataset_json(test_path(paste0("testdata/", df_name, ".json"))) + orig_df <- haven::read_xpt(test_path(paste0("testdata/", df_name, ".xpt"))) df_metadata <- readRDS(test_path("testdata/dm_metadata.Rds")) # create dataset json object - ds_json <- dataset_json(df_from_json, "IG.DM", "DM", "Demographics", df_metadata) - ds_json <- set_test_sdtm_metadata(ds_json) + ds_json <- dataset_json( + orig_df, + file_oid = "www.cdisc.org/StudyMSGv2/1/Define-XML_2.1.0/2024-08-05/dm", + last_modified = "2020-08-21T09:14:29", + originator = "CDISC SDTM MSG Team", + sys = "SAS on X64_10PRO", + sys_version = "9.0401M7", + study = "cdisc.com/CDISCPILOT01", + metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", + metadata_ref = "define.xml", + item_oid = "IG.DM", + name = "DM", + dataset_label = "Demographics", + columns = df_metadata + ) # write json to disk json_location <- paste0(df_name,".json") @@ -62,25 +68,35 @@ test_that("write_dataset_json matches the original json", { comp <- jsonlite::read_json(json_location) expected <- jsonlite::read_json(test_path("testdata/dm.json")) - # remove fileOID and creationDateTime, this will alway differ - # remove asOfDateTime, this is not in adsl.json (to confirm if extensible) - comp$fileOID <- NULL - expected$fileOID <- NULL - comp$asOfDateTime <- NULL - expected$asOfDateTime <- NULL - comp$creationDateTime <- NULL - expected$creationDateTime <- NULL + + # remove datasetJSONCreationDateTime, this will always differ + comp$datasetJSONCreationDateTime <- NULL + expected$datasetJSONCreationDateTime <- NULL expect_equal(comp, expected) # ta df_name <- "ta" - df_from_json <- read_dataset_json(test_path(paste0("testdata/", df_name, ".json"))) + orig_df <- haven::read_xpt(test_path(paste0("testdata/", df_name, ".xpt"))) df_metadata <- readRDS(test_path("testdata/ta_metadata.Rds")) # create dataset json object - ds_json <- dataset_json(df_from_json, "IG.TA", "TA", "Trial Arms", df_metadata, data_type="referenceData") - ds_json <- set_test_sdtm_metadata(ds_json) + ds_json <- dataset_json( + orig_df, + file_oid = "www.cdisc.org/StudyMSGv2/1/Define-XML_2.1.0/2024-08-05/ta", + last_modified = "2020-08-21T09:14:26", + originator = "CDISC SDTM MSG Team", + sys = "SAS on X64_10PRO", + sys_version = "9.0401M7", + study = "cdisc.com/CDISCPILOT01", + metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", + metadata_ref = "define.xml", + item_oid = "IG.TA", + name = "TA", + dataset_label = "Trial Arms", + ref_data = TRUE, + columns = df_metadata + ) # write json to disk json_location <- paste0(df_name,".json") @@ -90,14 +106,9 @@ test_that("write_dataset_json matches the original json", { comp <- jsonlite::read_json(json_location) expected <- jsonlite::read_json(test_path("testdata/ta.json")) - # remove fileOID and creationDateTime, this will alway differ - # remove asOfDateTime, this is not in adsl.json (to confirm if extensible) - comp$fileOID <- NULL - expected$fileOID <- NULL - comp$asOfDateTime <- NULL - expected$asOfDateTime <- NULL - comp$creationDateTime <- NULL - expected$creationDateTime <- NULL + # remove datasetJSONCreationDateTime, this will always differ + comp$datasetJSONCreationDateTime <- NULL + expected$datasetJSONCreationDateTime <- NULL expect_equal(comp, expected) }) @@ -110,12 +121,27 @@ test_that("write_dataset_json errors are thrown properly", { expect_error({ df_name <- "ta" - df_from_json <- read_dataset_json(test_path(paste0("testdata/", df_name, ".json"))) + orig_df <- haven::read_xpt(test_path(paste0("testdata/", df_name, ".xpt"))) df_metadata <- readRDS(test_path("testdata/ta_metadata.Rds")) # create dataset json object - ds_json <- dataset_json(df_from_json, "IG.TA", "TA", "Trial Arms", df_metadata, data_type="referenceData") - ds_json <- set_test_sdtm_metadata(ds_json) + + ds_json <- dataset_json( + orig_df, + file_oid = "www.cdisc.org/StudyMSGv2/1/Define-XML_2.1.0/2024-08-05/ta", + last_modified = "2020-08-21T09:14:26", + originator = "CDISC SDTM MSG Team", + sys = "SAS on X64_10PRO", + sys_version = "9.0401M7", + study = "cdisc.com/CDISCPILOT01", + metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", + metadata_ref = "define.xml", + item_oid = "IG.TA", + name = "TA", + dataset_label = "Trial Arms", + ref_data = TRUE, + columns = df_metadata + ) write_dataset_json(ds_json, file = "not/a/valid/directory/ta.json")}, "Folder supplied to `file` does not exist" ) diff --git a/tests/testthat/testdata/adsl.json b/tests/testthat/testdata/adsl.json index cb7d856..8e571fe 100644 --- a/tests/testthat/testdata/adsl.json +++ b/tests/testthat/testdata/adsl.json @@ -1 +1 @@ -{"datasetJSONCreationDateTime":"2024-08-05T10:08:53","datasetJSONVersion":"1.1.0","fileOID":"www.cdisc.org/StudyMSGv1/1/Define-XML_2.1.0/2024-08-05/adsl","dbLastModifiedDateTime":"2024-08-05T10:08:46","originator":"CDISC ADaM MSG Team","sourceSystem":{"name":"SAS on X64_10PRO","version":"9.0401M7"},"studyOID":"TDF_ADaM.ADaMIG.1.1","metaDataVersionOID":"MDV.TDF_ADaM.ADaMIG.1.1","metaDataRef":"define.xml","itemGroupOID":"IG.ADSL","isReferenceData":false,"records":254,"name":"ADSL","label":"Subject-Level Analysis","columns":[{"itemOID":"ITEMGROUPDATASEQ","name":"ITEMGROUPDATASEQ","label":"Record Identifier","dataType":"integer"},{"itemOID":"IT.ADSL.STUDYID","name":"STUDYID","label":"Study Identifier","dataType":"string","length":12},{"itemOID":"IT.ADSL.USUBJID","name":"USUBJID","label":"Unique Subject Identifier","dataType":"string","length":11,"keySequence":1},{"itemOID":"IT.ADSL.SUBJID","name":"SUBJID","label":"Subject Identifier for the Study","dataType":"string","length":4},{"itemOID":"IT.ADSL.SITEID","name":"SITEID","label":"Study Site Identifier","dataType":"string","length":3},{"itemOID":"IT.ADSL.SITEGR1","name":"SITEGR1","label":"Pooled Site Group 1","dataType":"string","length":3},{"itemOID":"IT.ADSL.ARM","name":"ARM","label":"Description of Planned Arm","dataType":"string","length":20},{"itemOID":"IT.ADSL.TRT01P","name":"TRT01P","label":"Planned Treatment for Period 01","dataType":"string","length":20},{"itemOID":"IT.ADSL.TRT01PN","name":"TRT01PN","label":"Planned Treatment for Period 01 (N)","dataType":"integer"},{"itemOID":"IT.ADSL.TRT01A","name":"TRT01A","label":"Actual Treatment for Period 01","dataType":"string","length":20},{"itemOID":"IT.ADSL.TRT01AN","name":"TRT01AN","label":"Actual Treatment for Period 01 (N)","dataType":"integer"},{"itemOID":"IT.ADSL.TRTSDT","name":"TRTSDT","label":"Date of First Exposure to Treatment","dataType":"date","targetDataType":"integer","displayFormat":"E8601DA."},{"itemOID":"IT.ADSL.TRTEDT","name":"TRTEDT","label":"Date of Last Exposure to Treatment","dataType":"date","targetDataType":"integer","displayFormat":"E8601DA."},{"itemOID":"IT.ADSL.TRTDURD","name":"TRTDURD","label":"Total Treatment Duration (Days)","dataType":"integer"},{"itemOID":"IT.ADSL.AVGDD","name":"AVGDD","label":"Avg Daily Dose (as planned)","dataType":"float"},{"itemOID":"IT.ADSL.CUMDOSE","name":"CUMDOSE","label":"Cumulative Dose (as planned)","dataType":"float"},{"itemOID":"IT.ADSL.AGE","name":"AGE","label":"Age","dataType":"integer"},{"itemOID":"IT.ADSL.AGEGR1","name":"AGEGR1","label":"Pooled Age Group 1","dataType":"string","length":5},{"itemOID":"IT.ADSL.AGEGR1N","name":"AGEGR1N","label":"Pooled Age Group 1 (N)","dataType":"integer"},{"itemOID":"IT.ADSL.AGEU","name":"AGEU","label":"Age Units","dataType":"string","length":5},{"itemOID":"IT.ADSL.RACE","name":"RACE","label":"Race","dataType":"string","length":32},{"itemOID":"IT.ADSL.RACEN","name":"RACEN","label":"Race (N)","dataType":"integer"},{"itemOID":"IT.ADSL.SEX","name":"SEX","label":"Sex","dataType":"string","length":1},{"itemOID":"IT.ADSL.ETHNIC","name":"ETHNIC","label":"Ethnicity","dataType":"string","length":22},{"itemOID":"IT.ADSL.SAFFL","name":"SAFFL","label":"Safety Population Flag","dataType":"string","length":1},{"itemOID":"IT.ADSL.ITTFL","name":"ITTFL","label":"Intent-To-Treat Population 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(kg/m^2)","dataType":"float"},{"itemOID":"IT.ADSL.BMIBLGR1","name":"BMIBLGR1","label":"Pooled Baseline BMI Group 1","dataType":"string","length":6},{"itemOID":"IT.ADSL.HEIGHTBL","name":"HEIGHTBL","label":"Baseline Height (cm)","dataType":"float"},{"itemOID":"IT.ADSL.WEIGHTBL","name":"WEIGHTBL","label":"Baseline Weight (kg)","dataType":"float"},{"itemOID":"IT.ADSL.EDUCLVL","name":"EDUCLVL","label":"Years of Education","dataType":"integer"},{"itemOID":"IT.ADSL.DISONSDT","name":"DISONSDT","label":"Date of Onset of Disease","dataType":"date","targetDataType":"integer","displayFormat":"E8601DA."},{"itemOID":"IT.ADSL.DURDIS","name":"DURDIS","label":"Duration of Disease (Months)","dataType":"float"},{"itemOID":"IT.ADSL.DURDSGR1","name":"DURDSGR1","label":"Pooled Disease Duration Group 1","dataType":"string","length":4},{"itemOID":"IT.ADSL.VISIT1DT","name":"VISIT1DT","label":"Date of Visit 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