updates for teal.slice (#73)

insightsengineering · Jun 22, 2022 · fc44939 · fc44939
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commit fc44939
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diff --git a/R/data_extract_filter_module.R b/R/data_extract_filter_module.R
@@ -119,8 +119,8 @@ data_extract_filter_srv <- function(id, datasets, filter) {
 #' @keywords internal
 #'
 #' @examples
-#' filtered_data <- teal.slice:::FilteredData$new()$set_dataset(
-#'   teal.data::dataset("iris", utils::head(iris))
+#' filtered_data <- teal.slice::init_filtered_data(
+#'   list(iris = list(dataset = utils::head(iris)))
 #' )
 #' filter <- filter_spec(vars = colnames(iris)[1])
 #' filter$dataname <- "iris"

diff --git a/R/data_extract_module.R b/R/data_extract_module.R
@@ -287,9 +287,10 @@ check_data_extract_spec_react <- function(datasets, data_extract) {
 #'   AGE = rpois(10, 30),
 #'   BMRKR1 = rlnorm(10)
 #' )
-#' data <- teal.data::teal_data(teal.data::dataset("ADSL", ADSL))
-#' datasets <- teal.slice:::filtered_data_new(data)
-#' teal.slice:::filtered_data_set(data, datasets)
+#' datasets <- teal.slice::init_filtered_data(
+#'   list(ADSL = list(dataset = ADSL, keys = c("STUDYID", "USUBJID"), parent = character(0))),
+#'   cdisc = TRUE
+#' )
 #'
 #' adsl_extract <- data_extract_spec(
 #'   dataname = "ADSL",
@@ -437,9 +438,10 @@ data_extract_srv <- function(id, datasets, data_extract_spec) {
 #'   BMRKR1 = rlnorm(10)
 #' )
 #'
-#' data <- teal.data::teal_data(teal.data::dataset("ADSL", ADSL))
-#' datasets <- teal.slice:::filtered_data_new(data)
-#' teal.slice:::filtered_data_set(data, datasets)
+#' datasets <- teal.slice::init_filtered_data(
+#'   list(ADSL = list(dataset = ADSL, keys = c("STUDYID", "USUBJID"), parent = character(0))),
+#'   cdisc = TRUE
+#' )
 #'
 #' xvar_extract <- data_extract_spec(
 #'   dataname = "ADSL",

diff --git a/R/data_merge_module.R b/R/data_merge_module.R
@@ -44,8 +44,7 @@
 #'   teal.data::cdisc_dataset("ADSL", ADSL),
 #'   teal.data::cdisc_dataset("ADLB", ADLB)
 #' )
-#' datasets <- teal.slice:::filtered_data_new(data)
-#' teal.slice:::filtered_data_set(data, datasets)
+#' datasets <- teal.slice::init_filtered_data(data)
 #'
 #' adsl_extract <- data_extract_spec(
 #'   dataname = "ADSL",
@@ -172,8 +171,7 @@ data_merge_module <- function(datasets,
 #'   teal.data::cdisc_dataset("ADSL", ADSL),
 #'   teal.data::cdisc_dataset("ADLB", ADLB)
 #' )
-#' datasets <- teal.slice:::filtered_data_new(data)
-#' teal.slice:::filtered_data_set(data, datasets)
+#' datasets <- teal.slice::init_filtered_data(data)
 #'
 #' adsl_extract <- data_extract_spec(
 #'   dataname = "ADSL",

diff --git a/R/format_data_extract.R b/R/format_data_extract.R
@@ -14,13 +14,9 @@
 #' )
 #'
 #' sample_filtered_data <- {
-#'   # create TealData
-#'   data <- teal.data::teal_data(teal.data::dataset("iris", iris))
-#'
-#'   # covert TealData to FilteredData
-#'   datasets <- teal.slice:::filtered_data_new(data)
-#'   teal.slice:::filtered_data_set(data, datasets)
-#'   datasets
+#'   teal.slice::init_filtered_data(
+#'     list(iris = list(dataset = iris))
+#'   )
 #' }
 #'
 #' if (interactive()) {

diff --git a/R/resolve_delayed.R b/R/resolve_delayed.R
@@ -12,11 +12,14 @@
 #' @examples
 #' library(scda)
 #'
-#' ds <- teal.slice:::FilteredData$new()
 #' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' attr(ADSL, "keys") <- teal.data::get_cdisc_keys("ADSL")
 #' shiny::isolate({
-#'   ds$set_dataset(teal.data::dataset("ADSL", ADSL))
+#'   ds <- teal.slice::init_filtered_data(
+#'     list(ADSL = list(
+#'       dataset = ADSL, keys = teal.data::get_cdisc_keys("ADSL"), parent = character(0)
+#'     )),
+#'     cdisc = TRUE
+#'   )
 #'
 #'   # value_choices example
 #'   v1 <- value_choices("ADSL", "SEX", "SEX")

diff --git a/man/data_extract_multiple_srv.Rd b/man/data_extract_multiple_srv.Rd
diff --git a/man/data_extract_srv.Rd b/man/data_extract_srv.Rd
diff --git a/man/data_merge_module.Rd b/man/data_merge_module.Rd
diff --git a/man/data_merge_srv.Rd b/man/data_merge_srv.Rd
diff --git a/man/format_data_extract.Rd b/man/format_data_extract.Rd
diff --git a/man/get_initial_filter_values.Rd b/man/get_initial_filter_values.Rd
diff --git a/man/resolve_delayed.Rd b/man/resolve_delayed.Rd
diff --git a/tests/testthat/shinytest/format_data_extract/app.R b/tests/testthat/shinytest/format_data_extract/app.R
@@ -5,10 +5,9 @@ simple_des <- teal.transform::data_extract_spec(
 )
 
 sample_filtered_data <- {
-  data <- teal.data::teal_data(teal.data::dataset("iris", iris))
-  datasets <- teal.slice:::filtered_data_new(data)
-  teal.slice:::filtered_data_set(data, datasets)
-  datasets
+  teal.slice::init_filtered_data(
+    list(iris = list(dataset = iris))
+  )
 }
 
 ui <- shiny::fluidPage(

diff --git a/tests/testthat/test-choices_selected.R b/tests/testthat/test-choices_selected.R
@@ -1,9 +1,7 @@
 adsl <- as.data.frame(as.list(setNames(nm = teal.data::get_cdisc_keys("ADSL"))))
 adtte <- as.data.frame(as.list(setNames(nm = teal.data::get_cdisc_keys("ADTTE"))))
 data <- teal.data::cdisc_data(teal.data::cdisc_dataset("ADSL", adsl), teal.data::cdisc_dataset("ADTTE", adtte))
-
-ds <- teal.slice:::CDISCFilteredData$new()
-isolate(teal.slice:::filtered_data_set(data, ds))
+ds <- teal.slice::init_filtered_data(data)
 
 vc_hard <- variable_choices("ADSL", subset = c("STUDYID", "USUBJID"))
 vc_hard_exp <- structure(

diff --git a/tests/testthat/test-data_extract_module.R b/tests/testthat/test-data_extract_module.R
@@ -144,7 +144,7 @@ testthat::test_that("Multiple datasets", {
 })
 
 testthat::test_that("get_initial_filters_values returns empty strings if vars_selected is NULL", {
-  filtered_data <- teal.slice:::FilteredData$new()
+  filtered_data <- teal.slice::init_filtered_data(list(iris = list(dataset = utils::head(iris))))
   filter <- filter_spec(vars = "test")
   filter$vars_selected <- NULL
   testthat::expect_equal(
@@ -155,7 +155,7 @@ testthat::test_that("get_initial_filters_values returns empty strings if vars_se
 
 testthat::test_that("get_initial_filters_values returns all column values and the selected option
   if choices is NULL", {
-  filtered_data <- teal.slice:::FilteredData$new()$set_dataset(teal.data::dataset("iris", utils::head(iris)))
+  filtered_data <- teal.slice::init_filtered_data(list(iris = list(dataset = utils::head(iris))))
   filter <- filter_spec(vars = colnames(iris)[1])
   filter$choices <- NULL
   filter$dataname <- "iris"
@@ -167,7 +167,7 @@ testthat::test_that("get_initial_filters_values returns all column values and th
 })
 
 testthat::test_that("get_initial_filters_values returns the selected and choices if they are not null", {
-  filtered_data <- teal.slice:::FilteredData$new()$set_dataset(teal.data::dataset("iris", utils::head(iris)))
+  filtered_data <- teal.slice::init_filtered_data(list(iris = list(dataset = utils::head(iris))))
   filter <- filter_spec(vars = colnames(iris)[length(colnames(iris))])
   filter$choices <- "setosa"
   filter$selected <- "setosa"

diff --git a/tests/testthat/test-data_extract_spec.R b/tests/testthat/test-data_extract_spec.R
@@ -188,9 +188,11 @@ test_that("delayed data_extract_spec works", {
   expect_equal(names(expected_spec), names(mix2))
   expect_equal(names(expected_spec), names(mix3))
 
-  ds <- teal.slice:::CDISCFilteredData$new()
   isolate({
-    ds$set_dataset(teal.data::cdisc_dataset("ADSL", ADSL))
+    ds <- teal.slice::init_filtered_data(
+      list(ADSL = list(dataset = ADSL, keys = c("USUBJID", "STUDYID"), parent = character(0))),
+      cdisc = TRUE
+    )
     expect_identical(expected_spec, resolve_delayed(delayed_spec, ds))
     expect_identical(expected_spec, resolve_delayed(mix1, ds))
     expect_identical(expected_spec, resolve_delayed(mix2, ds))
@@ -213,8 +215,7 @@ data <- teal.data::cdisc_data(
   teal.data::cdisc_dataset("ADTTE", adtte)
 )
 
-ds <- teal.slice:::CDISCFilteredData$new()
-isolate(teal.slice:::filtered_data_set(data, ds))
+ds <- teal.slice::init_filtered_data(data)
 
 vc_hard <- variable_choices("ADSL", subset = c("STUDYID", "USUBJID"))
 vc_hard_exp <- structure(

diff --git a/tests/testthat/test-data_extract_srv.R b/tests/testthat/test-data_extract_srv.R
@@ -1,8 +1,10 @@
 adsl_df <- as.data.frame(as.list(stats::setNames(nm = teal.data::get_cdisc_keys("ADSL"))))
 adsl <- teal.data::cdisc_dataset("ADSL", adsl_df)
 
-datasets <- teal.slice:::CDISCFilteredData$new()
-datasets$set_dataset(adsl)
+datasets <- teal.slice::init_filtered_data(
+  list(ADSL = list(dataset = adsl_df, keys = teal.data::get_cdisc_keys("ADSL"), parent = character(0))),
+  cdisc = TRUE
+)
 
 adsl_extract <- data_extract_spec(
   dataname = "ADSL",
@@ -103,8 +105,9 @@ testthat::test_that("data_extract_srv throws if data_extract_spec's dataname is
   )
 })
 
-filtered_data <- teal.slice:::FilteredData$new()
-filtered_data$set_dataset(teal.data::dataset("iris", iris))
+filtered_data <- teal.slice::init_filtered_data(
+  list(iris = list(dataset = iris))
+)
 
 testthat::test_that("data_extract_multiple_srv accepts a named list of `data_extract_spec`", {
   shiny::withReactiveDomain(
@@ -188,7 +191,7 @@ testthat::test_that("data_extract_multiple_srv throws if data_extract is not a n
   shiny::withReactiveDomain(
     domain = shiny::MockShinySession$new(),
     expr = testthat::expect_error(
-      data_extract_multiple_srv(list(1), datasets = teal.slice:::FilteredData$new()),
+      data_extract_multiple_srv(list(1), datasets = teal.slice::init_filtered_data(list(iris = list(dataset = iris)))),
       regexp = "Assertion on 'data_extract' failed: Must have names"
     )
   )

diff --git a/tests/testthat/test-data_merge_srv.R b/tests/testthat/test-data_merge_srv.R
@@ -7,10 +7,7 @@ adsl <- teal.data::cdisc_dataset("ADSL", adsl)
 adlb <- teal.data::cdisc_dataset("ADLB", adlb)
 data <- teal.data::cdisc_data(adsl, adlb)
 
-datasets_used <- teal.slice:::CDISCFilteredData$new()
-
-datasets_used$set_dataset(adsl)
-datasets_used$set_dataset(adlb)
+datasets_used <- teal.slice::init_filtered_data(data)
 
 adsl_data_extract_srv_output <-
   list(

diff --git a/tests/testthat/test-delayed_data_extract.R b/tests/testthat/test-delayed_data_extract.R
@@ -9,9 +9,7 @@ data <- teal.data::cdisc_data(
   teal.data::cdisc_dataset("ADTTE", ADTTE)
 )
 
-
-ds <- teal.slice:::CDISCFilteredData$new()
-isolate(teal.slice:::filtered_data_set(data, ds))
+ds <- teal.slice::init_filtered_data(data)
 
 vc_hard <- variable_choices("ADSL", subset = c("STUDYID", "USUBJID"))
 vc_hard_exp <- structure(
@@ -67,8 +65,7 @@ test_that("Delayed data extract - single data connector with two scda dataset co
     connector$pull()
   }
   # test delayed data extract
-  ds <- teal.slice:::CDISCFilteredData$new()
-  isolate(teal.slice:::filtered_data_set(data, ds))
+  ds <- teal.slice::init_filtered_data(data)
 
   ADSL <- data$get_dataset("ADSL")$get_raw_data() # nolint
   ADAE <- data$get_dataset("ADAE")$get_raw_data() # nolint
@@ -102,8 +99,7 @@ test_that("Delayed choices selected - single data connector with two scda datase
   for (connector in data$get_connectors()) {
     connector$pull()
   }
-  ds <- teal.slice:::CDISCFilteredData$new()
-  isolate(teal.slice:::filtered_data_set(data, ds))
+  ds <- teal.slice::init_filtered_data(data)
 
   ADSL <- data$get_dataset("ADSL")$get_raw_data() # nolint
   choices_expected <- variable_choices(ADSL, key = teal.data::get_cdisc_keys("ADSL"))
@@ -151,8 +147,7 @@ test_that("Delayed data extract - filtered", {
   for (connector in data$get_connectors()) {
     connector$pull()
   }
-  ds <- teal.slice:::CDISCFilteredData$new()
-  isolate(teal.slice:::filtered_data_set(data, ds))
+  ds <- teal.slice::init_filtered_data(data)
 
   ADSL <- data$get_dataset("ADSL")$get_raw_data() # nolint
   ADRS <- data$get_dataset("ADRS")$get_raw_data() # nolint
@@ -238,8 +233,7 @@ test_that("Delayed extract filter concatenated - single data connector with two
   for (connector in data$get_connectors()) {
     connector$pull()
   }
-  ds <- teal.slice:::CDISCFilteredData$new()
-  isolate(teal.slice:::filtered_data_set(data, ds))
+  ds <- teal.slice::init_filtered_data(data)
 
   ADSL <- data$get_dataset("ADSL")$get_raw_data() # nolint
   ADRS <- data$get_dataset("ADRS")$get_raw_data() # nolint
@@ -351,8 +345,7 @@ test_that("Delayed extract two filters - single data connector with two scda dat
   for (connector in data$get_connectors()) {
     connector$pull()
   }
-  ds <- teal.slice:::CDISCFilteredData$new()
-  isolate(teal.slice:::filtered_data_set(data, ds))
+  ds <- teal.slice::init_filtered_data(data)
 
   ADSL <- data$get_dataset("ADSL")$get_raw_data() # nolint
   ADRS <- data$get_dataset("ADRS")$get_raw_data() # nolint
@@ -416,7 +409,7 @@ test_that("Delayed extract two filters - single data connector with two scda dat
 test_that("Delayed extract - TealData with single dataset and multiple connectors", {
   adsl <- teal.data::dataset(
     dataname = "ADSL",
-    synthetic_cdisc_data("latest")$adsl,
+    scda::synthetic_cdisc_data("latest")$adsl,
     keys = teal.data::get_cdisc_keys("ADSL"),
     code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl",
     label = "ADSL"
@@ -475,8 +468,7 @@ test_that("Delayed extract - TealData with single dataset and multiple connector
   for (connector in data$get_connectors()) {
     connector$pull()
   }
-  ds <- teal.slice:::CDISCFilteredData$new()
-  isolate(teal.slice:::filtered_data_set(data, ds))
+  ds <- teal.slice::init_filtered_data(data)
 
   ADSL <- data$get_dataset("ADSL")$get_raw_data() # nolint
   ADRS <- data$get_dataset("ADRS")$get_raw_data() # nolint