Using ParallelLogger's JSON functions to store attributes. Fixes #54

OHDSI · Mar 29, 2023 · 33b6872 · 33b6872
1 parent 09d73a0
commit 33b6872
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Showing 3 changed files with 10 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,8 @@ Imports:
   pillar,
   glue,
   tidyselect,
-  jsonlite
+  jsonlite,
+  ParallelLogger
 Suggests:
   testthat,
   dbplyr,

diff --git a/R/LoadingSaving.R b/R/LoadingSaving.R
@@ -63,7 +63,8 @@ saveAndromeda <- function(andromeda, fileName, overwrite = TRUE) {
   attribs <- attributes(andromeda)
   attribs[["class"]] <- attribs[["path"]] <- attribs[["names"]] <- attribs[["env"]] <- attribs[[".xData"]] <- NULL
   attributesFileName <- file.path(tempdir(), "user-defined-attributes.json")
-  jsonlite::write_json(attribs, attributesFileName)
+  ParallelLogger::saveSettingsToJson(attribs, attributesFileName)
+  # jsonlite::write_json(attribs, attributesFileName, pretty = TRUE, force = TRUE, null = "null", auto_unbox = TRUE)
 
   tableDirs <- list.dirs(attr(andromeda, "path"), recursive = FALSE)
   zip::zipr(fileName, c(attributesFileName, tableDirs), compression_level = 2)
@@ -115,7 +116,8 @@ loadAndromeda <- function(fileName) {
   }
   class(andr) <- andrClass
 
-  attributes <- jsonlite::read_json(file.path(path, "user-defined-attributes.json"), simplifyVector = TRUE)
+  attributes <- ParallelLogger::loadSettingsFromJson(file.path(path, "user-defined-attributes.json"))
+  # attributes <- jsonlite::read_json(file.path(path, "user-defined-attributes.json"), simplifyVector = TRUE)
   on.exit(unlink(file.path(path, "user-defined-attributes.json")))
   for (nm in names(attributes)) {
     attr(andr, nm) <- attributes[[nm]]

diff --git a/tests/testthat/test-loadingSaving.R b/tests/testthat/test-loadingSaving.R
@@ -8,7 +8,9 @@ test_that("Saving and loading", {
   expect_true("table" %in% names(andromeda))
   iris1 <- andromeda$table %>% collect()
 
-  attr(andromeda, "metaData") <- list(x = 1)
+  s3Object <- list(a = 1)
+  class(s3Object) <- "MyClass"
+  attr(andromeda, "metaData") <- list(x = 1, y = list(s3Object))
 
   fileName <- tempfile(fileext = ".zip")
   fileName <- file.path(.getAndromedaTempFolder(), "asdf.zip")
@@ -27,6 +29,7 @@ test_that("Saving and loading", {
   expect_equivalent(iris1, iris2)
   expect_false(is.null(attr(andromeda2, "metaData")))
   expect_equal(attr(andromeda2, "metaData")$x, 1)
+  expect_equal(class(attr(andromeda2, "metaData")$y[[1]]), "MyClass")
 
   expect_error(capture.output(saveAndromeda(andromeda2, fileName, overwrite = TRUE)), NA)