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198 Include user's card labels when generating the report #336

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merged 12 commits into from
Oct 13, 2023
Merged

198 Include user's card labels when generating the report #336

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7239549
add card_template function and allow to pass label to reporter card c…
kartikeyakirar Oct 4, 2023
b1f8bef
adding Rd file
kartikeyakirar Oct 4, 2023
9ada482
Adding unit-test and removing default parameter defined in function c…
kartikeyakirar Oct 5, 2023
e04793a
fixing lintr
kartikeyakirar Oct 5, 2023
b577b49
removing default values from card_template in barplot.
kartikeyakirar Oct 5, 2023
f5d7a2e
Merge b577b49b5d0896c14dc75d12af5f0d99e0af56bc into 3d16439ea447c4a0a…
kartikeyakirar Oct 5, 2023
3f050d3
[skip actions] Restyle files
github-actions[bot] Oct 5, 2023
3bd4c23
'Empty-Commit'
kartikeyakirar Oct 5, 2023
0bac7e4
removing namespace call
kartikeyakirar Oct 6, 2023
f7f7240
removing card_template function and unit-test
kartikeyakirar Oct 11, 2023
0fbb71f
renaming to report_card_template
kartikeyakirar Oct 12, 2023
068f65a
removing namespace call
kartikeyakirar Oct 12, 2023
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11 changes: 6 additions & 5 deletions R/barplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -190,11 +190,12 @@ srv_g_barplot <- function(id,

### REPORTER
if (with_reporter) {
card_fun <- function(comment) {
card <- teal::TealReportCard$new()
card$set_name("Barplot")
card$append_text("Barplot", "header2")
card$append_fs(filter_panel_api$get_filter_state())
card_fun <- function(comment, label) {
card <- card_template(
title = "Barplot",
label = label,
filter_panel_api = filter_panel_api
)
card$append_text("Selected Options", "header3")
encodings_list <- list(
"Experiment:",
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11 changes: 6 additions & 5 deletions R/boxplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -185,11 +185,12 @@ srv_g_boxplot <- function(id,

### REPORTER
if (with_reporter) {
card_fun <- function(comment) {
card <- teal::TealReportCard$new()
card$set_name("Boxplot")
card$append_text("Boxplot", "header2")
card$append_fs(filter_panel_api$get_filter_state())
card_fun <- function(comment, label) {
card <- card_template(
title = "Boxplot",
label = label,
filter_panel_api = filter_panel_api
)
card$append_text("Selected Options", "header3")
encodings_list <- list(
"Experiment:",
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11 changes: 6 additions & 5 deletions R/forestplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -230,11 +230,12 @@ srv_g_forest_tte <- function(id,

### REPORTER
if (with_reporter) {
card_fun <- function(comment) {
card <- teal::TealReportCard$new()
card$set_name("Forest Plot")
card$append_text("Forest Plot", "header2")
card$append_fs(filter_panel_api$get_filter_state())
card_fun <- function(comment, label) {
card <- card_template(
title = "Forest Plot",
label = label,
filter_panel_api = filter_panel_api
)
card$append_text("Selected Options", "header3")
encodings_list <- list(
"Experiment:",
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11 changes: 6 additions & 5 deletions R/km.R
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Original file line number Diff line number Diff line change
Expand Up @@ -222,11 +222,12 @@ srv_g_km <- function(id,

### REPORTER
if (with_reporter) {
card_fun <- function(comment) {
card <- teal::TealReportCard$new()
card$set_name("Kaplan-Meier Plot")
card$append_text("Kaplan-Meier Plot", "header2")
card$append_fs(filter_panel_api$get_filter_state())
card_fun <- function(comment, label) {
card <- card_template(
title = "Kaplan-Meier Plot",
label = label,
filter_panel_api = filter_panel_api
)
card$append_text("Selected Options", "header3")
encodings_list <- list(
"Experiment:",
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11 changes: 6 additions & 5 deletions R/pca.R
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Original file line number Diff line number Diff line change
Expand Up @@ -357,11 +357,12 @@ srv_g_pca <- function(id,

### REPORTER
if (with_reporter) {
card_fun <- function(comment) {
card <- teal::TealReportCard$new()
card$set_name("PCA")
card$append_text("PCA", "header2")
card$append_fs(filter_panel_api$get_filter_state())
card_fun <- function(comment, label) {
card <- card_template(
title = "PCA",
label = label,
filter_panel_api = filter_panel_api
)
card$append_text("Selected Options", "header3")
if (input$tab_selected == "PCA") {
encodings_list <- list(
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13 changes: 7 additions & 6 deletions R/quality.R
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Original file line number Diff line number Diff line change
Expand Up @@ -353,12 +353,13 @@ srv_g_quality <- function(id,

### REPORTER
if (with_reporter) {
card_fun <- function(comment) {
card <- teal::TealReportCard$new()
card$set_name("Quality Control Plot")
card$append_text("Quality Control Plot", "header2")
card$append_text(tools::toTitleCase(input$plot_type), "header3")
card$append_fs(filter_panel_api$get_filter_state())
card_fun <- function(comment, label) {
card <- card_template(
title = "Quality Control Plot",
label = label,
description = tools::toTitleCase(input$plot_type),
filter_panel_api = filter_panel_api
)
card$append_text("Selected Options", "header3")
encodings_list <- list(
"Experiment:",
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11 changes: 6 additions & 5 deletions R/scatterplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -185,11 +185,12 @@ srv_g_scatterplot <- function(id,

### REPORTER
if (with_reporter) {
card_fun <- function(comment) {
card <- teal::TealReportCard$new()
card$set_name("Scatter Plot")
card$append_text("Scatter Plot", "header2")
card$append_fs(filter_panel_api$get_filter_state())
card_fun <- function(comment, label) {
card <- card_template(
title = "Scatter Plot",
label = label,
filter_panel_api = filter_panel_api
)
card$append_text("Selected Options", "header3")
encodings_list <- list(
"Experiment:",
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27 changes: 27 additions & 0 deletions R/utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -77,3 +77,30 @@ include_js_files <- function(pattern = "*") { # nolint
)
return(singleton(lapply(js_files, includeScript)))
}

#' Template function to generate reporter card for `teal.modules.hermes`
#' @param title (`character(1)`) title of the card (unless overwritten by label)
#' @param label (`character(1)`) label provided by the user when adding the card
#' @param description (`character(1)`) optional additional description
#' @param filter_panel_api (`FilterPanelAPI`) object with API that allows the generation
#' of the filter state in the report
#'
#' @return (`TealReportCard`) populated with a title, description and filter state
#'
#' @keywords internal
card_template <- function(title, label, description = NULL, filter_panel_api) {
checkmate::assert_string(title)
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sorry can we please take out the checkmate:: name space thing since we import the whole of it?

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putting package name in front of package function improves the process of debugging if you debug the function interactively

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teal is also imported as a whole but we do put :: in front of teal function names https://github.com/search?q=repo%3Ainsightsengineering%2Fteal.modules.hermes%20%3A%3A&type=code

teal.modules.hermes/R/scatterplot.R

Line 48 in 3d16439

teal::module(

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yeah we should also take out the teal:: bits please. thanks!

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@kartikeyakirar have you seen this conversation about teal

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@kartikeyakirar kartikeyakirar Oct 12, 2023 •
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Okay, I will take out teal:: call as well.

Edit : Namespace calls are throughout the package, and it's not within the scope of this task to eliminate all of them. However, I will remove teal::report_card_template. As for the rest, I will put the task to handle them separately .

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Here is task : #337

checkmate::assert_string(label)
checkmate::assert_string(description, null.ok = TRUE)
checkmate::assert_class(filter_panel_api, classes = "FilterPanelAPI")

card <- teal::TealReportCard$new()
title <- if (label == "") title else label
card$set_name(title)
card$append_text(title, "header2")
if (!is.null(description)) {
card$append_text(description, "header3")
}
card$append_fs(filter_panel_api$get_filter_state())
card
}
11 changes: 6 additions & 5 deletions R/volcanoplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -207,11 +207,12 @@ srv_g_volcanoplot <- function(id,

### REPORTER
if (with_reporter) {
card_fun <- function(comment) {
card <- teal::TealReportCard$new()
card$set_name("Volcano Plot")
card$append_text("Volcano Plot", "header2")
card$append_fs(filter_panel_api$get_filter_state())
card_fun <- function(comment, label) {
card <- card_template(
title = "Volcano Plot",
label = label,
filter_panel_api = filter_panel_api
)
card$append_text("Selected Options", "header3")
encodings_list <- list(
"Experiment:",
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25 changes: 25 additions & 0 deletions man/card_template.Rd
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25 changes: 25 additions & 0 deletions tests/testthat/test-utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -18,3 +18,28 @@ test_that("h_extract_words works as expected", {
"All elements must have at least 1 characters, but element 1 has 0 characters."
)
})

testthat::test_that("card_template function returns TealReportCard object with appropriate content and labels", {
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fd <- teal.slice::init_filtered_data(list(iris = list(dataset = iris)))
filter_panel_api <- teal.slice::FilterPanelAPI$new(fd)

card <- shiny::isolate(card_template(
title = "Card title",
label = "Card label",
description = NULL,
filter_panel_api = filter_panel_api
))
testthat::expect_s3_class(card, c("TealReportCard"))
testthat::expect_equal(card$get_name(), "Card label")
testthat::expect_length(card$get_content(), 3)

card <- shiny::isolate(card_template(
title = "Card title",
label = "",
description = "Description text",
filter_panel_api = filter_panel_api
))
testthat::expect_s3_class(card, c("TealReportCard"))
testthat::expect_equal(card$get_name(), "Card title")
testthat::expect_length(card$get_content(), 4)
})