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370 again integration test failures because of snapshot changes #371

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merged 6 commits into from
Mar 25, 2024
+958 −139
Merged

370 again integration test failures because of snapshot changes #371

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b25bed7
add .test argument
Mar 18, 2024
cb53cae
update boxplot and forest
Mar 22, 2024
b272b45
update remaining modules
Mar 22, 2024
c4e6e63
Merge branch 'main' into 370-again-integration-test-failures@main
Mar 22, 2024
f8b5dc9
use message
Mar 22, 2024
fe5aec6
remove unused files
Mar 25, 2024
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1 change: 1 addition & 0 deletions R/argument_convention.R
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@
#' @param plot_width (`list`)\cr list of integers to set the default, minimum,
#' and maximum plot width.
#' @param filter_panel_api (`FilterPanelAPI`)\cr object describing the actual filter panel API.
#' @param .test (`flag`)\cr whether to display the internal structure of the plot for testing purposes.
#'
#' @name module_arguments
#' @keywords internal
Expand Down
35 changes: 27 additions & 8 deletions R/barplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,29 +34,33 @@ tm_g_barplot <- function(label,
Max = matrixStats::colMaxs
),
pre_output = NULL,
post_output = NULL) {
post_output = NULL,
.test = FALSE) {
message("Initializing tm_g_barplot")
assert_string(label)
assert_string(mae_name)
assert_character(exclude_assays)
assert_summary_funs(summary_funs)
assert_tag(pre_output, null.ok = TRUE)
assert_tag(post_output, null.ok = TRUE)
assert_flag(.test)

module(
label = label,
server = srv_g_barplot,
server_args = list(
mae_name = mae_name,
exclude_assays = exclude_assays,
summary_funs = summary_funs
summary_funs = summary_funs,
.test = .test
),
ui = ui_g_barplot,
ui_args = list(
mae_name = mae_name,
summary_funs = summary_funs,
pre_output = pre_output,
post_output = post_output
post_output = post_output,
.test = .test
),
datanames = mae_name
)
Expand All @@ -69,7 +73,8 @@ ui_g_barplot <- function(id,
mae_name,
summary_funs,
pre_output,
post_output) {
post_output,
.test = FALSE) {
ns <- NS(id)
teal.widgets::standard_layout(
encoding = tags$div(
Expand Down Expand Up @@ -101,7 +106,10 @@ ui_g_barplot <- function(id,
)
)
),
output = teal.widgets::plot_with_settings_ui(ns("plot")),
output = div(
if (.test) verbatimTextOutput(ns("table")) else NULL,
teal.widgets::plot_with_settings_ui(ns("plot"))
),
pre_output = pre_output,
post_output = post_output
)
Expand All @@ -116,11 +124,13 @@ srv_g_barplot <- function(id,
reporter,
mae_name,
exclude_assays,
summary_funs) {
summary_funs,
.test = FALSE) {
with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
assert_class(filter_panel_api, "FilterPanelAPI")
checkmate::assert_class(data, "reactive")
checkmate::assert_class(shiny::isolate(data()), "teal_data")
assert_flag(.test)
moduleServer(id, function(input, output, session) {
output$experiment_ui <- renderUI({
experimentSpecInput(session$ns("experiment"), data, mae_name)
Expand Down Expand Up @@ -189,6 +199,13 @@ srv_g_barplot <- function(id,
plot_r = plot_r
)

if (.test) {
table_r <- reactive({
str(layer_data(plot_r()))
})
output$table <- renderPrint(table_r())
}

### REPORTER
if (with_reporter) {
card_fun <- function(comment, label) {
Expand Down Expand Up @@ -230,6 +247,7 @@ srv_g_barplot <- function(id,
card$append_text("Comment", "header3")
card$append_text(comment)
}

card
}
teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
Expand All @@ -246,14 +264,15 @@ srv_g_barplot <- function(id,
#' if (interactive()) {
#' sample_tm_g_barplot()
#' }
sample_tm_g_barplot <- function() {
sample_tm_g_barplot <- function(.test = FALSE) {
data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
app <- teal::init(
data = data,
modules = teal::modules(
tm_g_barplot(
label = "barplot",
mae_name = "MAE"
mae_name = "MAE",
.test = .test
)
)
)
Expand Down
33 changes: 25 additions & 8 deletions R/boxplot.R
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -35,29 +35,33 @@ tm_g_boxplot <- function(label,
Max = matrixStats::colMaxs
),
pre_output = NULL,
post_output = NULL) {
post_output = NULL,
.test = FALSE) {
message("Initializing tm_g_boxplot")
assert_string(label)
assert_string(mae_name)
assert_character(exclude_assays, any.missing = FALSE)
assert_summary_funs(summary_funs, null.ok = TRUE)
assert_tag(pre_output, null.ok = TRUE)
assert_tag(post_output, null.ok = TRUE)
assert_flag(.test)

teal::module(
label = label,
server = srv_g_boxplot,
server_args = list(
mae_name = mae_name,
summary_funs = summary_funs,
exclude_assays = exclude_assays
exclude_assays = exclude_assays,
.test = .test
),
ui = ui_g_boxplot,
ui_args = list(
mae_name = mae_name,
summary_funs = summary_funs,
pre_output = pre_output,
post_output = post_output
post_output = post_output,
.test = .test
),
datanames = mae_name
)
Expand All @@ -70,7 +74,8 @@ ui_g_boxplot <- function(id,
mae_name,
summary_funs,
pre_output,
post_output) {
post_output,
.test = FALSE) {
ns <- NS(id)
teal.widgets::standard_layout(
encoding = tags$div(
Expand All @@ -97,7 +102,10 @@ ui_g_boxplot <- function(id,
)
)
),
output = teal.widgets::plot_with_settings_ui(ns("plot")),
output = div(
if (.test) verbatimTextOutput(ns("table")) else NULL,
teal.widgets::plot_with_settings_ui(ns("plot"))
),
pre_output = pre_output,
post_output = post_output
)
Expand All @@ -112,7 +120,8 @@ srv_g_boxplot <- function(id,
reporter,
mae_name,
exclude_assays,
summary_funs) {
summary_funs,
.test = FALSE) {
with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
assert_class(filter_panel_api, "FilterPanelAPI")
checkmate::assert_class(data, "reactive")
Expand Down Expand Up @@ -184,6 +193,13 @@ srv_g_boxplot <- function(id,
plot_r = plot_r
)

if (.test) {
table_r <- reactive({
str(layer_data(plot_r()))
})
output$table <- renderPrint(table_r())
}

### REPORTER
if (with_reporter) {
card_fun <- function(comment, label) {
Expand Down Expand Up @@ -247,14 +263,15 @@ srv_g_boxplot <- function(id,
#' if (interactive()) {
#' sample_tm_g_boxplot()
#' }
sample_tm_g_boxplot <- function() {
sample_tm_g_boxplot <- function(.test = FALSE) {
data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
app <- teal::init(
data = data,
modules = teal::modules(
tm_g_boxplot(
label = "boxplot",
mae_name = "MAE"
mae_name = "MAE",
.test = .test
)
)
)
Expand Down
37 changes: 27 additions & 10 deletions R/forestplot.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,8 @@ tm_g_forest_tte <- function(label,
pre_output = NULL,
post_output = NULL,
plot_height = c(600L, 200L, 2000L),
plot_width = c(1360L, 500L, 2000L)) {
plot_width = c(1360L, 500L, 2000L),
.test = FALSE) {
message("Initializing tm_g_forest_tte")
assert_string(label)
assert_string(adtte_name)
Expand All @@ -63,6 +64,7 @@ tm_g_forest_tte <- function(label,
assert_summary_funs(summary_funs)
assert_tag(pre_output, null.ok = TRUE)
assert_tag(post_output, null.ok = TRUE)
assert_flag(.test)

teal::module(
label = label,
Expand All @@ -74,15 +76,17 @@ tm_g_forest_tte <- function(label,
exclude_assays = exclude_assays,
summary_funs = summary_funs,
plot_height = plot_height,
plot_width = plot_width
plot_width = plot_width,
.test = .test
),
ui = ui_g_forest_tte,
ui_args = list(
adtte_name = adtte_name,
mae_name = mae_name,
summary_funs = summary_funs,
pre_output = pre_output,
post_output = post_output
post_output = post_output,
.test = .test
),
datanames = c(adtte_name, mae_name)
)
Expand All @@ -96,7 +100,8 @@ ui_g_forest_tte <- function(id,
mae_name,
summary_funs,
pre_output,
post_output) {
post_output,
.test = FALSE) {
ns <- NS(id)
teal.widgets::standard_layout(
encoding = tags$div(
Expand All @@ -120,7 +125,10 @@ ui_g_forest_tte <- function(id,
)
)
),
output = teal.widgets::plot_with_settings_ui(ns("plot")),
output = div(
if (.test) verbatimTextOutput(ns("table")) else NULL,
teal.widgets::plot_with_settings_ui(ns("plot"))
),
pre_output = pre_output,
post_output = post_output
)
Expand All @@ -139,7 +147,8 @@ srv_g_forest_tte <- function(id,
exclude_assays,
summary_funs,
plot_height,
plot_width) {
plot_width,
.test = FALSE) {
with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
assert_class(filter_panel_api, "FilterPanelAPI")
checkmate::assert_class(data, "reactive")
Expand Down Expand Up @@ -217,8 +226,8 @@ srv_g_forest_tte <- function(id,
})

forest_plot <- reactive({
result <- result()
tern::g_forest(result)
res <- result()
tern::g_forest(res)
})

pws <- teal.widgets::plot_with_settings_srv(
Expand All @@ -228,6 +237,13 @@ srv_g_forest_tte <- function(id,
width = plot_width
)

if (.test) {
table_r <- reactive({
rtables::as_result_df(result())
})
output$table <- renderPrint(table_r())
}

### REPORTER
if (with_reporter) {
card_fun <- function(comment, label) {
Expand Down Expand Up @@ -285,7 +301,7 @@ srv_g_forest_tte <- function(id,
#' if (interactive()) {
#' sample_tm_g_forest_tte()
#' }
sample_tm_g_forest_tte <- function() { # nolint
sample_tm_g_forest_tte <- function(.test = FALSE) { # nolint
data <- teal_data()
data <- within(data, {
ADTTE <- teal.modules.hermes::rADTTE %>% # nolint
Expand All @@ -302,7 +318,8 @@ sample_tm_g_forest_tte <- function() { # nolint
tm_g_forest_tte(
label = "forest",
adtte_name = "ADTTE",
mae_name = "MAE"
mae_name = "MAE",
.test = .test
)
)
)
Expand Down
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