Refactor

[gogonzo]

Part of insightsengineering/teal#937
Other PRs insightsengineering/teal#899 insightsengineering/teal.slice#440

install

Installation code

staged.dependencies::dependency_table(
  project = "insightsengineering/teal@https://github.com",
  project_type = "repo@host",
  ref = "refactor",
  verbose = 1
) |> staged.dependencies::install_deps()

ddl class

unfold

Small class which contains ui and server. server calls run_ddl which evaluates a code using input and create teal_data object. Function ddl accepts several arguments which are used to generate proper ui and server.

Above diagram depict how class works. Please follow steps below and look at the diagram.

1. One needs to specify ddl arguments to fit someone's needs. Take for example custom_connector. Let's assume that we need to call scda::synthetic_cdisc_data('latest') for two datasets.

data_code = paste(
    "adsl <- scda::synthetic_cdisc_data('latest')$adsl",
    "adtte<- scda::synthetic_cdisc_data('version')$adtte",
    collapse = "\n"
  )
)

Imagine that above datasets are on the remote server so we need to call open_conn function and close after pull. Imagine that open_conn and close_conn are in some external package.

code = paste(c(
  "open_conn(username = input$username, password = input$password)",
  "adsl <- scda::synthetic_cdisc_data('latest')$adsl",
  "adtte<- scda::synthetic_cdisc_data('version')$adtte",
  "close_conn()"
  ),
  collapse = "\n"
)

username and password should be specified by the app user. To do so we need to create ui which will create username and password inputs which are used during evaluation of above code.

ui = function(id) {
  ns <- NS(id)
  tagList(
    textInput(ns("username"), label = "Username"),
      passwordInput(ns("password"), label = "Password"),
      actionButton(ns("submit"), label = "Submit")
  )
}

If we have ui we need also server to utilize input. When submit button is clicked all input values are passed to ddl_run where all magic happens. ddl_run executes the code and substitutes all input$<name> with equivalent input_list element.

submit_button_server <- function(id) {
  moduleServer(id, function(input, output, session) {
    tdata <- eventReactive(input$submit, {
      req(input$pass)
      ddl_run(input_list = reactiveValuesToList(input))
    })

    # would need to make sure we handle reactivity correctly here as teal::init expects not reactive tdata...
    return(tdata)
  })
}

Because user username and password is not something we would like to include in the show R code. We need to replace them with some other code which can be run by anyone who receives the code. To replace args with some desired value or call we use offline_args to substitute code with these.

offline_args = list(
  username = quote(askpass::askpass("Please enter username")),
  password = quote(askpass::askpass("Please enter password"))
)  

At this point ddl_run evaluated "online" code, and has environment with the results of the evaluation. Also "offline" code is available after substitution. At the end teal_data_new is constructed from data and offline code

teal_data_new(env_list, code = masked_code, join_keys)

⚠️ As one can see ddl_run require only input_list. It is a simplification for potential app developer who doesn't need to handle additional arguments (code, input_mask) in the server. Consequence of this simplification is that server specified in ddl() have an enclosing environment changed to the environment where ddl_run, code, input_mask is available. Another consequence is that ddl_run theoretically doesn't exist anywhere - it is created on the fly when ddl object is created. It means that developing own ddl connector in external "pkg" can't use private functions from that "pkg".

Example connector app

R code

custom_password_connector <- function(datanames) {
  ddl(
    # code to be run when app user presses submit
    code = paste(
      c(
        "conn <- open_conn(username = input$username, password = input$password)",
        sprintf(
          "%1$s <- scda::synthetic_cdisc_data('latest')$%1$s",
          datanames
        ),
        "close_conn()"
      ),
      collapse = "\n"
    ),

    # arguments used for show R code
    mask_args = list(
      username = quote(askpass::askpass()),
      password = quote(askpass::askpass())
    ),

    # ui they wish to use for the loading data
    ui = function(id) {
      ns <- NS(id)
      tagList(
        textInput(ns("username"), label = "Username"),
        passwordInput(ns("password"), label = "Password"),
        actionButton(ns("submit"), label = "Submit")
      )
    },
    datanames = datanames
  )
}

pkgload::load_all("teal.data")
pkgload::load_all("teal")
library(shiny)

x <- custom_password_connector(c("adsl", "adtte", "adrs"))


app <- shinyApp(
  ui = fluidPage(
    fluidRow(
      column(3, h1("User Inputs"), x$ui(id = "custom_ui")),
      column(9, h1("R code"), verbatimTextOutput("output"))
    )
  ),
  server = function(input, output, session) {
    loaded_data <- x$server(id = "custom_ui", x = x)
    output$output <- renderText({
      req(loaded_data())
      teal.code::get_code(loaded_data()) |> paste(collapse = "\n")
    })
  }
)

shiny::runApp(app)

Example teal app with connector

teal app code

use teal.data, teal and teal.slice from refactor branch

# options(teal.log_level = "TRACE", teal.show_js_log = TRUE)
options("teal.bs_theme" = bslib::bs_theme(version = 3))

library(shiny)
library(scda)
library(scda.2022)
library(teal.data)
library(teal.transform)
pkgload::load_all("teal.data")
pkgload::load_all("teal.slice")
pkgload::load_all("teal")

library(teal.modules.general)

funny_module <- function(label = "Filter states", datanames = "all") {
  checkmate::assert_string(label)
  module(
    label = label,
    datanames = datanames,
    ui = function(id, ...) {
      ns <- NS(id)
      div(
        h2("The following filter calls are generated:"),
        verbatimTextOutput(ns("filter_states")),
        verbatimTextOutput(ns("filter_calls")),
        actionButton(ns("reset"), "reset_to_default")
      )
    },
    server = function(input, output, session, data, filter_panel_api) {
      checkmate::assert_class(data, "tdata")
      observeEvent(input$reset, set_filter_state(filter_panel_api, default_filters))
      output$filter_states <- renderPrint({
        logger::log_trace("rendering text1")
        filter_panel_api %>% get_filter_state()
      })
      output$filter_calls <- renderText({
        logger::log_trace("rendering text2")
        attr(data, "code")()
      })
    }
  )
}

custom_password_connector <- function(datanames) {
  ddl(
    # code to be run when app user presses submit
    code = paste(
      c(
        "conn <- open_conn(username = input$username, password = input$password)",
        sprintf(
          "%1$s <- scda::synthetic_cdisc_data('latest')$%1$s",
          datanames
        ),
        "close_conn()"
      ),
      collapse = "\n"
    ),

    # arguments used for show R code
    mask_args = list(
      username = quote(askpass::askpass()),
      password = quote(askpass::askpass())
    ),

    # ui they wish to use for the loading data
    ui = function(id) {
      ns <- NS(id)
      tagList(
        textInput(ns("username"), label = "Username"),
        passwordInput(ns("password"), label = "Password"),
        actionButton(ns("submit"), label = "Submit")
      )
    },
    datanames = datanames
  )
}
data <- custom_password_connector(c("adsl", "adtte", "adrs"))

app <- init(
  data = data,
  modules = modules(
    funny_module("funny"),
    funny_module("funny2", datanames = "adtte") # will limit datanames to ADTTE and ADSL (parent)
  )
)

runApp(app)

teal app with teal_data

App code

# options(teal.log_level = "TRACE", teal.show_js_log = TRUE)
options("teal.bs_theme" = bslib::bs_theme(version = 3))

library(shiny)
library(scda)
library(scda.2022)
library(teal.data)
library(teal.transform)
pkgload::load_all("teal.data")
pkgload::load_all("teal.slice")
pkgload::load_all("teal")
library(teal.modules.general)

funny_module <- function(label = "Filter states", datanames = "all") {
  checkmate::assert_string(label)
  module(
    label = label,
    datanames = datanames,
    ui = function(id, ...) {
      ns <- NS(id)
      div(
        h2("The following filter calls are generated:"),
        verbatimTextOutput(ns("filter_states")),
        verbatimTextOutput(ns("filter_calls")),
        actionButton(ns("reset"), "reset_to_default")
      )
    },
    server = function(input, output, session, data, filter_panel_api) {
      checkmate::assert_class(data, "tdata")
      observeEvent(input$reset, set_filter_state(filter_panel_api, default_filters))
      output$filter_states <- renderPrint({
        logger::log_trace("rendering text1")
        filter_panel_api %>% get_filter_state()
      })
      output$filter_calls <- renderText({
        logger::log_trace("rendering text2")
        attr(data, "code")()
      })
    }
  )
}

data <- cdisc_data(
  ADSL = synthetic_cdisc_data("latest")$adsl,
  ADTTE = synthetic_cdisc_data("latest")$adtte,
  ADRS = synthetic_cdisc_data("latest")$adrs,
  code = '
    ADSL <- synthetic_cdisc_data("latest")$adsl
    ADTTE <- synthetic_cdisc_data("latest")$adtte
    ADRS <- synthetic_cdisc_data("latest")$adrs
  '
)

app <- init(
  data = data,
  modules = modules(
    funny_module("funny"),
    funny_module("funny2", datanames = "ADTTE") # will limit datanames to ADTTE and ADSL (parent)
  )
)

runApp(app)

teal.gallery examples

• exploratory app with tdata https://github.com/insightsengineering/teal.gallery/blob/refactor/exploratory/app.R
• basic teal app with ddl https://github.com/insightsengineering/teal.gallery/blob/refactor/basic-teal/app.R

Internal Connectors

insightsengineering/nestdevs-tasks#38

What's next

To complete insightsengineering/teal#937 we need to do following:

Match arguments across all reproducible objects/classes (ddl, qenv, teal_data):

• Don't allow to specify initial env and a code teal.code#145
• change new_teal_data arguments #169
• Introduce within.qenv teal.code#127

Other:

• [Feature request] Rework <teal_module>$server to get teal_data object teal#904
• Remove access to data from UI modules teal.slice#132
• [Bug]: Concept of delayed creates indirect dependency between data and UI elements teal.transform#111
• Remove insertUI in the teal::init teal#669
• Simplify data constructor for join_keys #162
• [Feature Request]: Make a data module teal#860
• (possibly) Refactor nested_tabs module teal#534

[m7pr]

Hi, I'm getting below, when I run Example connector app or Example teal app with connector

Listening on http://127.0.0.1:7985
Warning in ddl_run(x = x, online_args = reactiveValuesToList(input)) :
  DDL code returned NULL. Returning empty tdata object
Warning in (function (..., join_keys = teal.data::join_keys(), code = "",  :
  Using TealDatasetConnector and TealDataset is deprecated, please just include data directly.
Warning: Error in <-: attempt to set an attribute on NULL

Had issues installing staged.dependencies openpharma/staged.dependencies#189
but after a 5th execution of the same code I managed to install it properly.

Result of staged.dependencies execution

x <-
  +   staged.dependencies::dependency_table(
    +        project = "insightsengineering/teal@https://github.com",
    +        project_type = "repo@host",
    +        ref = "refactor",
    +        verbose = 1
    +      )
fetch https://github.com/insightsengineering/teal.git in cache directory...
- checkout branch origin/refactor in cache directory...
fetch https://github.com/insightsengineering/teal.widgets.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.code.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.data.git in cache directory...
- checkout branch origin/refactor in cache directory...
fetch https://github.com/insightsengineering/teal.slice.git in cache directory...
- checkout branch origin/refactor in cache directory...
fetch https://github.com/insightsengineering/teal.transform.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.logger.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.reporter.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.modules.general.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.modules.clinical.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.osprey.git in cache directory...
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fetch https://github.com/insightsengineering/teal.goshawk.git in cache directory...
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fetch https://github.com/insightsengineering/hermes.git in cache directory...
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fetch https://github.com/insightsengineering/scda.2022.git in cache directory...
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fetch https://github.com/insightsengineering/teal.devel.git in cache directory...
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Current cache directory: C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache
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> x |> staged.dependencies::install_deps()
Processing packages in order: formatters, rtables, teal.widgets, teal.code, teal.logger, teal.data, teal.slice, teal.transform, teal.reporter, teal
* installing *source* package 'formatters' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'ncol' from package 'base' in package 'formatters'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (formatters)
* installing *source* package 'rtables' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'nrow' from package 'base' in package 'rtables'
Creating a generic function for 'rbind' from package 'base' in package 'rtables'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rtables)
* installing *source* package 'teal.widgets' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (teal.widgets)
Skipping installation of C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.code_f5c7ee90093dd244b11b1acde2d5098a since same commit sha already installed
Skipping installation of C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.logger_db3be93ac2413ef16521b0cf8fe202ad since same commit sha already installed
* installing *source* package 'teal.data' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning message:
  package 'shiny' was built under R version 4.3.1 
Warning: replacing previous import 'teal.code::show' by 'shinyjs::show' when loading 'teal.data'
Warning in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) :
  'package:stats' may not be available when loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package 'shiny' was built under R version 4.3.1
Warning: replacing previous import 'teal.code::show' by 'shinyjs::show' when loading 'teal.data'
** testing if installed package can be loaded from final location
Warning: package 'shiny' was built under R version 4.3.1
Warning: replacing previous import 'teal.code::show' by 'shinyjs::show' when loading 'teal.data'
** testing if installed package keeps a record of temporary installation path
* DONE (teal.data)
* installing *source* package 'teal.slice' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
  package 'shiny' was built under R version 4.3.1 
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package 'shiny' was built under R version 4.3.1
Warning: S3 method 'init_filtered_data.TealData' was declared in NAMESPACE but not found
** testing if installed package can be loaded from final location
Warning: package 'shiny' was built under R version 4.3.1
Warning: S3 method 'init_filtered_data.TealData' was declared in NAMESPACE but not found
** testing if installed package keeps a record of temporary installation path
* DONE (teal.slice)
* installing *source* package 'teal.transform' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (teal.transform)
* installing *source* package 'teal.reporter' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (teal.reporter)
* installing *source* package 'teal' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
  1: package 'shiny' was built under R version 4.3.1 
2: replacing previous import 'teal.code::show' by 'shinyjs::show' when loading 'teal.data' 
3: S3 method 'init_filtered_data.TealData' was declared in NAMESPACE but not found 
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package 'shiny' was built under R version 4.3.1
Warning: replacing previous import 'teal.code::show' by 'shinyjs::show' when loading 'teal.data'
Warning: S3 method 'init_filtered_data.TealData' was declared in NAMESPACE but not found
** testing if installed package can be loaded from final location
Warning: package 'shiny' was built under R version 4.3.1
Warning: replacing previous import 'teal.code::show' by 'shinyjs::show' when loading 'teal.data'
Warning: S3 method 'init_filtered_data.TealData' was declared in NAMESPACE but not found
** testing if installed package keeps a record of temporary installation path
* DONE (teal)
Processed packages in order: formatters, rtables, teal.widgets, teal.code, teal.logger, teal.data, teal.slice, teal.transform, teal.reporter, teal
package_name
1      formatters
2         rtables
3    teal.widgets
4       teal.code
5     teal.logger
6       teal.data
7      teal.slice
8  teal.transform
9   teal.reporter
10           teal
cache_dir
1      C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_formatters_2af660375fccd6c369329f665710ecae
2         C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_rtables_f0f6291eb2b1f6976bb05ff26dfa212d
3    C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.widgets_8f92a3d7b00ae5fadadf0ffc4492c7f2
4       C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.code_f5c7ee90093dd244b11b1acde2d5098a
5     C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.logger_db3be93ac2413ef16521b0cf8fe202ad
6       C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.data_39f26acbb991125a81ff5392c742cf86
7      C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.slice_69fabf5d920c35ab0e950fac1a49b372
8  C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.transform_7dbb21e492260b8f5bd20354278faa2c
9   C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal.reporter_2c5a990a10b0c9b8f7bccf13bd04db2a
10           C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache/insightsengineering_teal_e38093f352c184cf676b1dd47551848c
actions     sha installable
1  install ebd84a1        TRUE
2  install e751f69        TRUE
3  install b4aae30        TRUE
4  install 760b73f        TRUE
5  install 203c910        TRUE
6  install 212806c        TRUE
7  install 450ddc0        TRUE
8  install 64b0bb9        TRUE
9  install d514cf3        TRUE
10 install e54a865        TRUE

[gogonzo]

@m7pr

I'm getting below, when I run Example connector app or Example teal app with connector

Yes, you typed any password. Message says that password is pass ;)

[m7pr]

So it looks like it did the job, but it thrown some other unrelated error that confused me?

[averissimo]

@m7pr I needed to add pkgload::load_all("teal.slice") to the examples for them to work

[m7pr]

I did checkout to refactor branch locally for teal, teal.slice and teal.data made pulls and build those packages locally. I thought staged.dependencies would do that for me. I actually think that pkgload::load_all('teal') was loading from improper branch on my local machine.

I was able to run the Example connector app

and Example teal app with connector

[chlebowa]

Suggested change

	if (!checkmate::test_names(names(data_objects), type = "named")) {
	stop("Dot (`...`) arguments on `teal_data()` must be named.")
	}
	checkmate::assert_names(names(data_objects), .var.name = "dot arguments (`...`) in `teal_data()`")

[averissimo]

Ah great!

The function I used before is the soon-to-be-deprecated assert_named() which had a non-descriptive error message (failed: Must have Object.), but this is much cleaner :-)

[vedhav]

I know it's still in the draft and looks like there do not seem to be major changes expected to the PR.

Can we update the _pkgdown.yml with the new exported functions and add some vignettes to explain the new functions?

[chlebowa]

The only use of this function that I found is in teal::init, which on this branch looks like this:

  if (!inherits(data, c("TealData", "tdata", "ddl"))) {
    data <- teal.data::to_relational_data(data = data)
  }

Methods for TealData and tdata are defined but not called.

Furthermore, the conversion is followed by an assertion:

checkmate::assert_multi_class(data, c("TealData", "tdata", "ddl"))

I don't know why a method for ddl is not defined, but assuming this is an oversight, I think it would be better to define to_relational_data.default that will raise an error on the lines of "don't know how to handle data of class <class>" and remove the assertion from init.

Since we are trying to simplify things, I would be partial to init only accepting tdata, actually.

[chlebowa]

I don't like the argument being named env it it only accepts a list.

[chlebowa]

Looks like teal_data returns tdata now, not TealData. Is the first part (if (checkmate::test_list(data_objects, types = c("TealDataConnector", "TealDataset", "TealDatasetConnector")))) is only for deprecation purposes? If so, there should be a warning there.

[gogonzo]

Closing this PR in favour of #171