Adds decorate functionality to module output #1357

gogonzo · 2024-09-30T08:21:56Z

Companion PRs:

🗃️ decorators feature branch teal.modules.general#795

example tmg app

pkgload::load_all("teal")
pkgload::load_all("teal.modules.general")
library(teal.widgets)

data <- teal_data()
data <- within(data, {
  require(nestcolor)
  ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys[c("ADSL")]

footnote_regression <- teal_transform_module(
  server = make_teal_transform_server(expression(
    plot <- plot + labs(caption = deparse(summary(fit)[[1]]))
  ))
)

fact_vars_adsl <- names(Filter(isTRUE, sapply(data[["ADSL"]], is.factor)))
vars <- choices_selected(variable_choices(data[["ADSL"]], fact_vars_adsl))

app <- init(
  data = data,
  modules = modules(
    tm_a_regression(
      label = "Regression",
      response = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = "BMRKR1",
          selected = "BMRKR1",
          multiple = FALSE,
          fixed = TRUE
        )
      ),
      regressor = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variables:",
          choices = variable_choices(data[["ADSL"]], c("AGE", "SEX", "RACE")),
          selected = "AGE",
          multiple = TRUE,
          fixed = FALSE
        )
      ),
      ggplot2_args = ggplot2_args(
        labs = list(subtitle = "Plot generated by Regression Module")
      ),
      decorators = list(footnote_regression)
    )
  )
)

shinyApp(app$ui, app$server)

…main

…er creation - some documentation - some todo's

R/modules.R

R/module_nested_tabs.R

R/modules.R

…_data_module

R/teal_transform_module.R

R/dummy_functions.R

R/module_teal_data.R

pawelru · 2024-11-21T17:07:54Z

R/module_transform_data.R

 #' @rdname module_transform_data
-ui_transform_data <- function(id, transformers = list(), class = "well") {
+ui_teal_transform_data <- function(id, transformators, class = "well") {


how about ui/srv_transform_teal_data

This is because of:

Module to transform reactive teal_data

I agree and the team as well, on it

Although this requires a bunch of changes, so no single commit to show. I'll make the change in teal and then apply in tmg

R/module_transform_data.R

R/module_nested_tabs.R

pawelru · 2024-11-21T17:25:51Z

R/teal_transform_module.R

+#' @name teal_transform_module
+#'
+#' @export
+teal_transform_module <- function(ui = NULL,


what is your opinion about putting package name in the function name? Can it be just transform_module()?

I'm a little bit confused what the convention is - also looking into other functions

I think it can, but we may want to do this in a different issue and apply the same convention package-wide.

If my memory serves me, weeks/months ago we were all discussing with you @pawelru that module and modules should have the teal_ prefix.

that's exactly the part that I'm currently struggle with :)

Naming convention could be improved, we can discuss it on another issue for sure

pawelru · 2024-11-21T17:27:25Z

vignettes/decorate-module-output.Rmd

+Decorator failures are managed by an internal `teal` mechanism called **trigger on success**, which ensures that the `data`
+object within the module remains intact. If a decorator fails, it will be ignored, and an appropriate error message will be displayed.


isn't it too technical?

The decorator is a technical feature of the framework. We need to go into some details.

I'm not too sure about what it means to "remain intact". @m7pr can you clarify as you were the last one to change this line 😅

Suggested change

Decorator failures are managed by an internal `teal` mechanism called **trigger on success**, which ensures that the `data`

object within the module remains intact. If a decorator fails, it will be ignored, and an appropriate error message will be displayed.

Decorator failures are managed by an internal `teal` mechanism called **trigger on success**, which ensures that the `data`

object within the module remains intact.

If a decorator fails, the outputs will not be shown, and an appropriate error message will be displayed.

Like the object will not be changed inside module/teal_data id the decorator produces an error : P

Co-authored-by: Pawel Rucki <[email protected]> Signed-off-by: André Veríssimo <[email protected]>

llrs-roche

Just a small suggestion for the vignette as I was reading & running it locally to understand this feature better.

llrs-roche · 2024-11-22T09:26:15Z

vignettes/decorate-module-output.Rmd

+
+Preserving the object's class during decoration is essential for compatibility. It ensures that the subsequent "display" logic can seamlessly handle both decorated and non-decorated objects.
+
+The decoration process can vary in complexity:


This list doesn't show up nicely on the browser on my computer:

I think it needs a new line before it:

Suggested change

The decoration process can vary in complexity:

The decoration process can vary in complexity:

Good catch!

My assumption was that this is automatically detected - it seems that it's not

markdownlint results

❯ markdownlint vignettes/decorate-module-output.Rmd vignettes/decorate-module-output.Rmd:15:98 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:15:81 MD013/line-length Line length [Expected: 80; Actual: 98] vignettes/decorate-module-output.Rmd:16:103 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:16:81 MD013/line-length Line length [Expected: 80; Actual: 103] vignettes/decorate-module-output.Rmd:17:208 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:17:81 MD013/line-length Line length [Expected: 80; Actual: 208] vignettes/decorate-module-output.Rmd:18:81 MD013/line-length Line length [Expected: 80; Actual: 108] vignettes/decorate-module-output.Rmd:22:81 MD013/line-length Line length [Expected: 80; Actual: 587] vignettes/decorate-module-output.Rmd:24:81 MD013/line-length Line length [Expected: 80; Actual: 597] vignettes/decorate-module-output.Rmd:26:81 MD013/line-length Line length [Expected: 80; Actual: 190] vignettes/decorate-module-output.Rmd:29:81 MD013/line-length Line length [Expected: 80; Actual: 120] vignettes/decorate-module-output.Rmd:29 MD032/blanks-around-lists Lists should be surrounded by blank lines [Context: "- **Simple Decorations**: Sing..."] vignettes/decorate-module-output.Rmd:30:81 MD013/line-length Line length [Expected: 80; Actual: 161] vignettes/decorate-module-output.Rmd:32:81 MD013/line-length Line length [Expected: 80; Actual: 290] vignettes/decorate-module-output.Rmd:38:81 MD013/line-length Line length [Expected: 80; Actual: 222] vignettes/decorate-module-output.Rmd:39:81 MD013/line-length Line length [Expected: 80; Actual: 272] vignettes/decorate-module-output.Rmd:41:81 MD013/line-length Line length [Expected: 80; Actual: 136] vignettes/decorate-module-output.Rmd:45:109 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:45:81 MD013/line-length Line length [Expected: 80; Actual: 109] vignettes/decorate-module-output.Rmd:48:81 MD013/line-length Line length [Expected: 80; Actual: 116] vignettes/decorate-module-output.Rmd:49:110 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:49:81 MD013/line-length Line length [Expected: 80; Actual: 110] vignettes/decorate-module-output.Rmd:50:213 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:50:81 MD013/line-length Line length [Expected: 80; Actual: 213] vignettes/decorate-module-output.Rmd:51:81 MD013/line-length Line length [Expected: 80; Actual: 98] vignettes/decorate-module-output.Rmd:55:81 MD013/line-length Line length [Expected: 80; Actual: 227] vignettes/decorate-module-output.Rmd:56:74 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:57:106 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:57:81 MD013/line-length Line length [Expected: 80; Actual: 106] vignettes/decorate-module-output.Rmd:78:62 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:79:73 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:80:81 MD013/line-length Line length [Expected: 80; Actual: 202] vignettes/decorate-module-output.Rmd:96:144 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:96:81 MD013/line-length Line length [Expected: 80; Actual: 144] vignettes/decorate-module-output.Rmd:97:126 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:97:81 MD013/line-length Line length [Expected: 80; Actual: 126] vignettes/decorate-module-output.Rmd:98:81 MD013/line-length Line length [Expected: 80; Actual: 180] vignettes/decorate-module-output.Rmd:126:209 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:126:81 MD013/line-length Line length [Expected: 80; Actual: 209] vignettes/decorate-module-output.Rmd:127:81 MD013/line-length Line length [Expected: 80; Actual: 193] vignettes/decorate-module-output.Rmd:149:80 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:150:81 MD013/line-length Line length [Expected: 80; Actual: 123] vignettes/decorate-module-output.Rmd:151:81 MD013/line-length Line length [Expected: 80; Actual: 133] vignettes/decorate-module-output.Rmd:152:81 MD013/line-length Line length [Expected: 80; Actual: 119] vignettes/decorate-module-output.Rmd:182:81 MD013/line-length Line length [Expected: 80; Actual: 123] vignettes/decorate-module-output.Rmd:183:81 MD013/line-length Line length [Expected: 80; Actual: 134] vignettes/decorate-module-output.Rmd:205:120 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:205:81 MD013/line-length Line length [Expected: 80; Actual: 120] vignettes/decorate-module-output.Rmd:206:80 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:210 MD012/no-multiple-blanks Multiple consecutive blank lines [Expected: 1; Actual: 2] vignettes/decorate-module-output.Rmd:212:81 MD013/line-length Line length [Expected: 80; Actual: 93] vignettes/decorate-module-output.Rmd:312 MD024/no-duplicate-heading Multiple headings with the same content [Context: "Example Module"] vignettes/decorate-module-output.Rmd:314:81 MD013/line-length Line length [Expected: 80; Actual: 308] vignettes/decorate-module-output.Rmd:406:81 MD013/line-length Line length [Expected: 80; Actual: 87] vignettes/decorate-module-output.Rmd:421 MD012/no-multiple-blanks Multiple consecutive blank lines [Expected: 1; Actual: 2] vignettes/decorate-module-output.Rmd:493 MD024/no-duplicate-heading Multiple headings with the same content [Context: "Application"]

markdownlint results without MD13 (line lenght) rule

❯ markdownlint vignettes/decorate-module-output.Rmd --disable MD013 vignettes/decorate-module-output.Rmd:15:98 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:16:103 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:17:208 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:29 MD032/blanks-around-lists Lists should be surrounded by blank lines [Context: "- **Simple Decorations**: Sing..."] vignettes/decorate-module-output.Rmd:45:109 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:49:110 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:50:213 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:56:74 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:57:106 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:78:62 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:79:73 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:96:144 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:97:126 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:126:209 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:149:80 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:205:120 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:206:80 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1] vignettes/decorate-module-output.Rmd:210 MD012/no-multiple-blanks Multiple consecutive blank lines [Expected: 1; Actual: 2] vignettes/decorate-module-output.Rmd:312 MD024/no-duplicate-heading Multiple headings with the same content [Context: "Example Module"] vignettes/decorate-module-output.Rmd:421 MD012/no-multiple-blanks Multiple consecutive blank lines [Expected: 1; Actual: 2] vignettes/decorate-module-output.Rmd:493 MD024/no-duplicate-heading Multiple headings with the same content [Context: "Application"]

Your observation is there - among tons of other things :)
markdownlint is designed for .md files. I believe that .Rmd should have a similar structure (if not identical) - worst case we would have to disable some of the rules. I'm thinking that we should configure our superlinter CI workflow to process .Rmd with markdownlint. Let me create an issue for this. For the time being - I would recommend to test it manually.

https://github.com/insightsengineering/idr-tasks/issues/823

Nice, the heading checks might help to structure better the vignettes or simplify the sections.
I think you meant to link to https://github.com/insightsengineering/idr-tasks/issues/823

llrs-roche · 2024-11-22T11:08:15Z

vignettes/decorate-module-output.Rmd

+    tm_decorated_plot("no-ui", decorators = list(static_decorator)),
+    tm_decorated_plot("lang", decorators = list(static_decorator_lang)),
+    tm_decorated_plot("interactive", decorators = list(interactive_decorator)),
+    tm_decorated_plot("interactive-from lang", decorators = list(interactive_decorator_lang)),


The interactive-from lang example doesn't change the axis labels (on current branch status):

decorator_interactive_from_lang.mp4

The interactive_decorator_lang decorator uses make_teal_transform_server which is also used by static_decorator ( used in no-ui tab example) but on that example there is no possible change on the axis by the app user.

Other examples showing how to use decorators to change the axis interactively via function or with an interactive decorator work though.

vignettes/decorate-module-output.Rmd

Co-authored-by: Marcin <[email protected]> Fixes comments on vignette example on #1357

dependabot-preview bot added 4 commits September 26, 2024 15:07

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b74d1f6

init

6835c18

WIP

9fc5923

Merge branch 'main' into 1187_decorate_output@main

9bc0405

gogonzo marked this pull request as draft September 30, 2024 08:22

github-actions bot and others added 7 commits September 30, 2024 08:23

[skip style] [skip vbump] Restyle files

9f4e6dd

multiple outputs

fa117d1

Merge remote-tracking branch 'origin/main' into 1187_decorate_output@…

ed29e78

…main

reshuffle validation of teal_transform_module

c214c25

don't display UI if not specified

5f7ab79

Dispatch in teal_transform_module constructor

898015f

- make_teal_transform_server to simplify teal_transform_module's serv…

b5cb59f

…er creation - some documentation - some todo's

gogonzo commented Oct 9, 2024

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gogonzo commented Oct 9, 2024

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gogonzo commented Oct 9, 2024

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move teal_transform_module to a new file instead of keeping with teal…

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…_data_module

kpagacz reviewed Oct 14, 2024

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