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qenv warnings #621

Merged
merged 14 commits into from
Oct 27, 2022
Merged

qenv warnings #621

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966a3fe
update
mhallal1 Sep 29, 2022
9643a65
disable
mhallal1 Sep 29, 2022
d6f58d8
Apply suggestions from code review
mhallal1 Sep 29, 2022
a5e3ef7
Update R/tm_g_pp_adverse_events.R
mhallal1 Sep 29, 2022
ad116d9
fix km plot
Sep 29, 2022
401bd8d
correct names
mhallal1 Sep 30, 2022
d22b3e0
fix tm_t_tte
mhallal1 Sep 30, 2022
db589f5
fixes
mhallal1 Oct 3, 2022
640c871
Merge branch 'teal_refactor@main' into 63_warnings@teal_refactor@main
Oct 13, 2022
f73a2df
simplify warnings
Oct 25, 2022
4464045
Merge branch 'teal_refactor@main' into 63_warnings@teal_refactor@main
Oct 25, 2022
24e3175
Merge branch 'teal_refactor@main' into 63_warnings@teal_refactor@main
Oct 26, 2022
fc0ee7b
add missing verbatim_popup_srv
gogonzo Oct 27, 2022
53c6384
Apply suggestions from code review
gogonzo Oct 27, 2022
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14 changes: 12 additions & 2 deletions R/tm_a_mmrm.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -803,7 +803,10 @@ ui_mmrm <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
),
pre_output = a$pre_output,
post_output = a$post_output
)
Expand Down Expand Up @@ -877,7 +880,7 @@ srv_mmrm <- function(id,
)

anl_merged_q <- reactive({
q1 <- teal.code::new_qenv(tdata2env(data), code = get_code(data))
q1 <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))
q2 <- teal.code::eval_code(q1, as.expression(anl_merge_inputs()$expr))
teal.code::eval_code(q2, as.expression(adsl_merge_inputs()$expr))
})
Expand Down Expand Up @@ -1440,6 +1443,13 @@ srv_mmrm <- function(id,
return(what_to_return)
})

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(all_code())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(all_code())))
)

# Show R code once button is pressed.
teal.widgets::verbatim_popup_srv(
id = "rcode",
Expand Down
14 changes: 12 additions & 2 deletions R/tm_g_barchart_simple.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -300,7 +300,10 @@ ui_g_barchart_simple <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")
),
pre_output = args$pre_output,
post_output = args$post_output
)
Expand Down Expand Up @@ -332,7 +335,7 @@ srv_g_barchart_simple <- function(id,
shiny::validate({
shiny::need(merge_inputs()$columns_source$x, "Please select an x-variable")
})
quo <- teal.code::new_qenv(tdata2env(data), code = get_code(data))
quo <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))
quo <- teal.code::eval_code(quo, as.expression(merge_inputs()$expr))
quo
})
Expand Down Expand Up @@ -481,6 +484,13 @@ srv_g_barchart_simple <- function(id,
width = plot_width
)

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(output_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(output_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(output_q())),
Expand Down
14 changes: 12 additions & 2 deletions R/tm_g_ci.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -352,7 +352,10 @@ ui_g_ci <- function(id, ...) { # nolint
selected = args$stat
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
),
pre_output = args$pre_output,
post_output = args$post_output
)
Expand Down Expand Up @@ -382,7 +385,7 @@ srv_g_ci <- function(id, # nolint

merged_data_q <- reactive(
teal.code::eval_code(
object = teal.code::new_qenv(tdata2env(data), code = get_code(data)),
object = teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
code = as.expression(merged_data()$expr)
)
)
Expand Down Expand Up @@ -450,6 +453,13 @@ srv_g_ci <- function(id, # nolint

plot_r <- shiny::reactive(output_q()[["gg"]])

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(output_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(output_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(output_q())),
Expand Down
16 changes: 13 additions & 3 deletions R/tm_g_forest_rsp.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -446,7 +446,10 @@ ui_g_forest_rsp <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
),
pre_output = a$pre_output,
post_output = a$post_output
)
Expand Down Expand Up @@ -513,7 +516,7 @@ srv_g_forest_rsp <- function(id,
)

anl_merged_q <- reactive({
q <- teal.code::new_qenv(tdata2env(data), code = get_code(data))
q <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))
q1 <- teal.code::eval_code(q, as.expression(anl_merged()$expr))
teal.code::eval_code(q1, as.expression(adsl_merged()$expr))
})
Expand Down Expand Up @@ -704,6 +707,13 @@ srv_g_forest_rsp <- function(id,
width = plot_width
)

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(output_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(output_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(output_q())),
Expand All @@ -725,7 +735,7 @@ srv_g_forest_rsp <- function(id,
card$append_text("Comment", "header3")
card$append_text(comment)
}
card$append_src(paste(teal.code::get_code(output_q()), collapse = "\n"))
card$append_src(paste(teal.code::get_code(output_q()), collapse = "\n"), dd = "")
card
}
teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
Expand Down
14 changes: 12 additions & 2 deletions R/tm_g_forest_tte.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -451,7 +451,10 @@ ui_g_forest_tte <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")
),
pre_output = a$pre_output,
post_output = a$post_output
)
Expand Down Expand Up @@ -520,7 +523,7 @@ srv_g_forest_tte <- function(id,
)

anl_merged_q <- reactive({
q <- teal.code::new_qenv(tdata2env(data), code = get_code(data))
q <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))
q1 <- teal.code::eval_code(q, as.expression(anl_merged()$expr))
teal.code::eval_code(q1, as.expression(adsl_merged()$expr))
})
Expand Down Expand Up @@ -637,6 +640,13 @@ srv_g_forest_tte <- function(id,
width = plot_width
)

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(output_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(output_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(output_q())),
Expand Down
14 changes: 12 additions & 2 deletions R/tm_g_ipp.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -443,7 +443,10 @@ ui_g_ipp <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")
),
pre_output = a$pre_output,
post_output = a$post_output
)
Expand Down Expand Up @@ -494,7 +497,7 @@ srv_g_ipp <- function(id,
)

anl_merged_q <- reactive({
q <- teal.code::new_qenv(tdata2env(data), code = get_code(data))
q <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))
q1 <- teal.code::eval_code(q, as.expression(anl_merged()$expr))
teal.code::eval_code(q1, as.expression(adsl_merged()$expr))
})
Expand Down Expand Up @@ -594,6 +597,13 @@ srv_g_ipp <- function(id,
width = plot_width
)

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(output_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(output_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(output_q())),
Expand Down
17 changes: 13 additions & 4 deletions R/tm_g_km.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -597,7 +597,10 @@ ui_g_km <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
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teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")
),
pre_output = a$pre_output,
post_output = a$post_output
)
Expand Down Expand Up @@ -660,7 +663,7 @@ srv_g_km <- function(id,

anl_merged_q <- reactive({
teal.code::eval_code(
teal.code::new_qenv(tdata2env(data), code = get_code(data)),
teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
code = as.expression(anl_merged()$expr)
)
})
Expand Down Expand Up @@ -696,13 +699,12 @@ srv_g_km <- function(id,
if (length(input_arm_var) > 0 && length(unique(adsl_filtered[[input_arm_var]])) == 1) {
validate_args <- append(validate_args, list(min_n_levels_armvar = NULL))
}
if (input$compare_arms) {
if (isTRUE(input$compare_arms)) {
validate_args <- append(
validate_args,
list(ref_arm = unlist(input$buckets$Ref), comp_arm = unlist(input$buckets$Comp))
)
}

do.call(what = "validate_standard_inputs", validate_args)

# validate xticks
Expand Down Expand Up @@ -789,6 +791,13 @@ srv_g_km <- function(id,
width = plot_width
)

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(output_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(output_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(output_q())),
Expand Down
14 changes: 12 additions & 2 deletions R/tm_g_lineplot.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -484,7 +484,10 @@ ui_g_lineplot <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")
),
pre_output = a$pre_output,
post_output = a$post_output
)
Expand Down Expand Up @@ -523,7 +526,7 @@ srv_g_lineplot <- function(id,
)

anl_merged_q <- reactive({
teal.code::new_qenv(tdata2env(data), code = get_code(data)) %>% teal.code::eval_code(as.expression(anl_merged_input()$expr))
teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)) %>% teal.code::eval_code(as.expression(anl_merged_input()$expr))
})

merged <- list(anl_input_r = anl_merged_input, anl_q_r = anl_merged_q)
Expand Down Expand Up @@ -613,6 +616,13 @@ srv_g_lineplot <- function(id,
width = plot_width
)

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(output_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(output_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(output_q())),
Expand Down
14 changes: 12 additions & 2 deletions R/tm_g_pp_adverse_events.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -392,7 +392,10 @@ ui_g_adverse_events <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")
),
pre_output = ui_args$pre_output,
post_output = ui_args$post_output
)
Expand Down Expand Up @@ -467,7 +470,7 @@ srv_g_adverse_events <- function(id,
join_keys = get_join_keys(data)
)

anl_merged_q <- reactive(teal.code::eval_code(teal.code::new_qenv(tdata2env(data), code = get_code(data)), as.expression(anl_merged()$expr)))
anl_merged_q <- reactive(teal.code::eval_code(teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)), as.expression(anl_merged()$expr)))

outputs_q <- shiny::reactive({
shiny::validate(shiny::need(patient_id(), "Please select a patient."))
Expand Down Expand Up @@ -545,6 +548,13 @@ srv_g_adverse_events <- function(id,
width = plot_width
)

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(outputs_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(outputs_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(outputs_q())),
Expand Down
14 changes: 12 additions & 2 deletions R/tm_g_pp_patient_timeline.R
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -687,7 +687,10 @@ ui_g_patient_timeline <- function(id, ...) {
)
)
),
forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("warning"), button_label = "Show Warnings"),
teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")
),
pre_output = ui_args$pre_output,
post_output = ui_args$post_output
)
Expand Down Expand Up @@ -761,7 +764,7 @@ srv_g_patient_timeline <- function(id,
)

merge_q_r <- reactive({
teal.code::new_qenv(tdata2env(data), code = get_code(data)) %>%
teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)) %>%
teal.code::eval_code(as.expression(merge_input_r()$expr))
})

Expand Down Expand Up @@ -882,6 +885,13 @@ srv_g_patient_timeline <- function(id,
width = plot_width
)

teal.widgets::verbatim_popup_srv(
id = "warning",
verbatim_content = reactive(teal.code::get_warnings(output_q())),
title = "Warning",
disabled = reactive(is.null(teal.code::get_warnings(output_q())))
)

teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(output_q())),
Expand Down
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