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Tdata in tealdata@main #212

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Tdata in tealdata@main #212

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838a0b4
init
mhallal1 Feb 24, 2023
3604a33
tests
mhallal1 Feb 24, 2023
e124c5b
Merge 3604a3380e642efe5d74661146cdcae4222f7b39 into abf51503ec187dde0…
mhallal1 Feb 24, 2023
4f67533
[skip actions] Restyle files
github-actions[bot] Feb 24, 2023
aec07a9
empty
mhallal1 Feb 27, 2023
987e71d
Merge remote-tracking branch 'origin/tdata_in_tealdata@main' into tda…
mhallal1 Feb 27, 2023
ad9dffa
fix
mhallal1 Feb 27, 2023
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2 changes: 1 addition & 1 deletion NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ S3method(init_filter_states,MultiAssayExperiment)
S3method(init_filter_states,SummarizedExperiment)
S3method(init_filter_states,data.frame)
S3method(init_filter_states,matrix)
S3method(init_filtered_data,TealData)
S3method(init_filtered_data,default)
S3method(init_filtered_data,tdata)
S3method(init_filtered_dataset,MultiAssayExperiment)
S3method(init_filtered_dataset,data.frame)
S3method(resolve_state,default)
Expand Down
59 changes: 33 additions & 26 deletions R/FilteredData-utils.R
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Expand Up @@ -27,29 +27,29 @@ init_filtered_data <- function(x, join_keys, code, cdisc, check) {

#' @keywords internal
#' @export
init_filtered_data.TealData <- function(x, # nolint
join_keys = x$get_join_keys(),
code = x$get_code_class(),
cdisc = FALSE,
check = x$get_check()) {
init_filtered_data.tdata <- function(x, # nolint
join_keys = attr(x, "join_keys"),
code = attr(x, "code")(),
cdisc = FALSE,
check = attr(x, "check")) {
cdisc <- length(join_keys$get_parents()) > 0
data_objects <- lapply(x$get_datanames(), function(dataname) {
dataset <- x$get_dataset(dataname)
data_objects <- lapply(names(x), function(dataname) {
dataset <- x[[dataname]]()

parent <- if (cdisc) join_keys$get_parent(dataname) else NULL

return_list <- list(
dataset = dataset$get_raw_data(),
keys = dataset$get_keys(),
metadata = dataset$get_metadata(),
label = dataset$get_dataset_label()
dataset = dataset,
keys = join_keys$get(dataname, dataname),
metadata = teal.data::get_metadata(x, dataname),
label = attr(x, "label")[["dataname"]]
)

if (cdisc) return_list[["parent"]] <- parent
return_list
})

names(data_objects) <- x$get_datanames()
names(data_objects) <- names(x)

init_filtered_data(
x = data_objects,
Expand Down Expand Up @@ -184,26 +184,33 @@ eval_expr_with_msg <- function(expr, env) {
#' )
#'
#' server <- function(input, output, session) {
#' observeEvent(input$hide_content,
#' {
#' shinyjs::hide("content")
#' toggle_icon("toggle_content", c("fa-angle-down", "fa-angle-right"), one_way = TRUE)
#' },
#' ignoreInit = TRUE
#' )
#'
#' observeEvent(input$hide_content, {
#' shinyjs::hide("content")
#' toggle_icon("toggle_content", c("fa-angle-down", "fa-angle-right"), one_way = TRUE)
#' }, ignoreInit = TRUE)
#'
#' observeEvent(input$show_content, {
#' shinyjs::show("content")
#' toggle_icon("toggle_content", c("fa-angle-right", "fa-angle-down"), one_way = TRUE)
#' }, ignoreInit = TRUE)
#' observeEvent(input$show_content,
#' {
#' shinyjs::show("content")
#' toggle_icon("toggle_content", c("fa-angle-right", "fa-angle-down"), one_way = TRUE)
#' },
#' ignoreInit = TRUE
#' )
#'
#' observeEvent(input$toggle_content, {
#' shinyjs::toggle("content")
#' toggle_icon("toggle_content", c("fa-angle-right", "fa-angle-down"))
#' }, ignoreInit = TRUE)
#' observeEvent(input$toggle_content,
#' {
#' shinyjs::toggle("content")
#' toggle_icon("toggle_content", c("fa-angle-right", "fa-angle-down"))
#' },
#' ignoreInit = TRUE
#' )
#'
#' output$printout <- renderPrint({
#' head(faithful, 10)
#' })
#'
#' }
#'
#' if (interactive()) {
Expand Down
35 changes: 21 additions & 14 deletions man/toggle_button.Rd
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14 changes: 7 additions & 7 deletions tests/testthat/test-CDISCFilteredData.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ get_cdisc_filtered_data <- function() {
data <- teal.data::cdisc_data(
teal.data::cdisc_dataset("ADSL", adsl),
teal.data::cdisc_dataset("ADAE", adae)
)
)$get_tdata()

list(ds = init_filtered_data(data), adsl = adsl, adae = adae)
list(ds = isolate(init_filtered_data(data)), adsl = adsl, adae = adae)
}

testthat::test_that("load and set_datasets", {
Expand Down Expand Up @@ -104,7 +104,7 @@ testthat::test_that("get_filterable_varnames does not return child duplicates",
)
data <- teal.data::cdisc_data(adsl, child)

fd <- init_filtered_data(data)
fd <- isolate(init_filtered_data(data$get_tdata()))
testthat::expect_identical(
fd$get_filterable_varnames("ADTTE"),
c("PARAMCD", "c")
Expand All @@ -124,7 +124,7 @@ testthat::test_that("get_filterable_varnames does not return child non-filterabl
)
data <- teal.data::cdisc_data(adsl, child)

fd <- init_filtered_data(data)
fd <- isolate(init_filtered_data(data$get_tdata()))

fd$set_filterable_varnames("ADTTE", c("PARAMCD", "STUDYID"))
testthat::expect_identical(
Expand All @@ -144,7 +144,7 @@ testthat::test_that("get_filterable_varnames return all filterable variables fro
)
data <- teal.data::cdisc_data(adsl, child)

fd <- init_filtered_data(data)
fd <- isolate(init_filtered_data(data$get_tdata()))

testthat::expect_identical(
fd$get_filterable_varnames("ADSL"),
Expand All @@ -170,7 +170,7 @@ testthat::test_that("get_filterable_varnames does not return duplicates from par
)
data <- teal.data::cdisc_data(adsl, child)

fd <- init_filtered_data(data)
fd <- isolate(init_filtered_data(data$get_tdata()))

fd$set_filterable_varnames("ADSL", c("a", "b"))

Expand All @@ -196,7 +196,7 @@ testthat::test_that(
)
data <- teal.data::cdisc_data(adsl, child)

fd <- init_filtered_data(data)
fd <- isolate(init_filtered_data(data$get_tdata()))
testthat::expect_warning(
shiny::isolate(fd$set_filter_state(list(ADTTE = list(USUBJID = "1")))),
"These columns filters were excluded: USUBJID from dataset ADTTE"
Expand Down
6 changes: 3 additions & 3 deletions tests/testthat/test-init_filtered_data.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
testthat::test_that("init_filtered_data accepts a TealData object", {
testthat::test_that("init_filtered_data accepts a tdata object of a tealData object", {
teal_data <- teal.data::teal_data(teal.data::dataset(dataname = "iris", x = iris))
testthat::expect_no_error(init_filtered_data(teal_data))
testthat::expect_no_error(isolate(init_filtered_data(teal_data$get_tdata())))
})

testthat::test_that("init_filtered_data accepts a CDISCTealData with mixed CDISC and Dataset", {
Expand All @@ -9,7 +9,7 @@ testthat::test_that("init_filtered_data accepts a CDISCTealData with mixed CDISC
teal.data::dataset(dataname = "iris", x = iris),
teal.data::cdisc_dataset("ADSL", adsl)
)
testthat::expect_no_error(init_filtered_data(teal_data))
testthat::expect_no_error(isolate(init_filtered_data(teal_data$get_tdata())))
})

testthat::test_that("init_filtered_data accepts a list of `data.frame` objects", {
Expand Down