Refactor #161

gogonzo · 2023-08-15T04:25:20Z

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.

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):

Other:

m7pr · 2023-08-23T11:43:48Z

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...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.goshawk.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.modules.hermes.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.modules.helios.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/rtables.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/nestcolor.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/tern.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/tern.mmrm.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/tern.gee.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/formatters.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/osprey.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/goshawk.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/hermes.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/helios.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/tern.rbmi.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/chevron.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/citril.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/scda.test.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/biomarker-catalog.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/tlg-catalog.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/rlistings.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/dunlin.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/citril.metadata.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/scda.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/scda.2022.git in cache directory...
- checkout branch origin/main in cache directory...
fetch https://github.com/insightsengineering/teal.devel.git in cache directory...
- checkout branch origin/main in cache directory...
Current cache directory: C:/Users/kosinsm4/Documents/.staged.dependencies/packages_cache
1 
2 
3 
4 
5 
6 
7 
8 
9 
> 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 · 2023-09-06T05:59:36Z

@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 · 2023-09-06T09:45:29Z

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

averissimo · 2023-09-06T13:27:21Z

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

R/cdisc_data.R

R/teal_data.R

m7pr · 2023-09-07T10:24:50Z

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 · 2023-09-09T12:50:52Z

R/cdisc_data.R

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


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()`")

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 · 2023-09-11T12:43:32Z

R/to_relational_data.R

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 · 2023-09-11T12:59:49Z

R/tdata.R

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

chlebowa · 2023-09-11T13:37:50Z

R/teal_data.R

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.

R/ddl.R

R/tdata.R

R/is_pulled.R

`ddl` implementation alternative to #161 . Complemented by [this PR](insightsengineering/teal#922). In order to simplify the user (app dev) experience, I tried to streamline the logic. In order to create a `ddl` connector module, one has to: 1. use `input_template` to create the module: enumerate input widgets 2. provide a function, `on_submit`, to be run when `"submit"` button is clicked; function takes input values wrapped in a list called `input` and body refers to input values with `input$<value>` or `input[["<value>"]]` 3. optionally provide mask for input values that will be used in code of resulting `tdata` object 4. specify names of data sets for compatibility with `teal` (I don't like it) 5. optionally specify join keys as one would previously, for compatibility with `teal`; defaults to empty `teal.data::join_keys()` When inputs are submitted, `on_submit` is passed to a function that extracts the body, substitutes `input` placeholders with input values and evaluates the code to obtain data sets in a separate environment. Then it replaces the input values in the code with ones provided in `mask` (if any) and uses the environment and the masked code to create `tdata`. Much like in the solution proposed on branch `refactor`, the user provides code to obtain data sets and replacements for input values, and data is created in separate environment, which is then used to create `tdata` with masked code. Unlike that solution, the user specifies everything in one place, rather than having to define module ui, module server that runs a post-processing function, the post-processing function itself, etc. This is easier to understand **for me**. Another difference is that the user provides code as code with `input$` references, not text with `glue` syntax (`{ value }`). This is done move focus to masking rather than have the user think about "online" and "offline" arguments. It also uses pure base R. #### MOCK DATABASE CONNECTION ``` pullme <- function(username, password) { if (username == "user" && password == "pass") { message("connection established") } else { stop("invalid credentials") } } closeme <- function() { message("connection closed") } ``` #### MODULE DEFINITION ``` library(shiny) thefun <- function(input) { on.exit(try(closeme())) pullme(username = input$user, password = input$pass) adsl <- scda::synthetic_cdisc_data('latest')$adsl adtte <- scda::synthetic_cdisc_data('latest')$adtte } themask <- list( user = quote(askpass("who are you?")), pass = quote(askpass("password please")) ) module <- input_template( on_submit = thefun, mask = themask, datanames = c("adsl", "adtte"), textInput("user", "username", value = "user", placeholder = "who goes there?"), passwordInput("pass", "password", value = "pass", placeholder = "friend or foe?"), actionButton("submit", "get it") ) ``` #### AN APP ``` devtools::load_all("../teal.slice") devtools::load_all("../teal") devtools::load_all(".") ui <- fluidPage( tagList( module$ui("id"), uiOutput("val") ) ) server <- function(input, output, session) { tdata <- module$server("id") output[["value"]] <- renderPrint({ tdata() }) output[["code"]] <- renderPrint({ cat(teal.code::get_code(tdata()), sep = "\n") }) output[["val"]] <- renderUI({ req(tdata()) tagList( verbatimTextOutput("value"), verbatimTextOutput("code") ) }) } if (interactive()) shinyApp(ui, server) ``` #### A TEAL APP ``` 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$filter_calls <- renderText({ logger::log_trace("rendering text2") attr(data, "code")() }) } ) } devtools::load_all("../teal.slice") devtools::load_all("../teal") devtools::load_all(".") app <- init( data = module, modules = modules( funny_module("funny1"), funny_module("funny2", datanames = "adtte") # will limit datanames to ADTTE and ADSL (parent) ) ) shinyApp(app$ui, app$server) ```

gogonzo · 2023-10-04T12:11:23Z

Closing this PR in favour of #171

gogonzo added 4 commits August 14, 2023 14:11

any data possible

e622149

Merge remote-tracking branch 'origin/main' into refactor

9827de3

Merge remote-tracking branch 'origin/main' into refactor

2daf83a

ddl

bef092f

gogonzo added the core label Aug 15, 2023

gogonzo and others added 3 commits August 15, 2023 04:25

Merge bef092f into ba573f2

3f723f3

[skip actions] Restyle files

5e3c0cb

adjust to teal

7429b55

gogonzo mentioned this pull request Aug 15, 2023

Prototype ddl + tdata #140

Closed

gogonzo and others added 3 commits August 15, 2023 15:32

fix

e964b95

Merge e964b95 into ba573f2

1b1ebc6

[skip actions] Restyle files

3f37efe

gogonzo marked this pull request as draft August 16, 2023 06:48

change arg names

212806c

This was referenced Aug 16, 2023

Remove insertUI in the teal::init insightsengineering/teal#669

Closed

[Feature request] Rework <teal_module>$server to get teal_data object insightsengineering/teal#904

Closed

donyunardi mentioned this pull request Aug 24, 2023

Refactor the data class in teal insightsengineering/nestdevs-tasks#41

Closed

Merge branch 'main' into refactor

7d9e2b0

averissimo reviewed Sep 6, 2023

View reviewed changes

R/cdisc_data.R Outdated Show resolved Hide resolved

averissimo reviewed Sep 6, 2023

View reviewed changes

R/teal_data.R Outdated Show resolved Hide resolved

cleanup builds

7edaf2a

@anverissimo review

b30029b

chlebowa reviewed Sep 9, 2023

View reviewed changes

vedhav self-requested a review September 11, 2023 12:11

vedhav reviewed Sep 11, 2023

View reviewed changes

chlebowa mentioned this pull request Sep 18, 2023

ddl alternative #167

Merged

chlebowa reviewed Sep 18, 2023

View reviewed changes

chlebowa reviewed Sep 21, 2023

View reviewed changes

R/tdata.R Outdated Show resolved Hide resolved

chlebowa reviewed Sep 22, 2023

View reviewed changes

R/tdata.R Outdated Show resolved Hide resolved

chlebowa reviewed Sep 22, 2023

View reviewed changes

R/is_pulled.R Outdated Show resolved Hide resolved

gogonzo and others added 10 commits September 28, 2023 06:59

Merge remote-tracking branch 'origin/main' into refactor

2248740

ddl WIP

6504197

POC

d067b93

tdata -> teal_data

56a7b2d

mask_args -> input_mask

f3876df

online_args -> input

c407adf

ddl_run - input can be of class "reactivevalues"

5443613

handling datanames information

48e0f3b

ddl from teal.data to teal

6b46e4c

gogonzo closed this Oct 4, 2023

gogonzo deleted the refactor branch October 4, 2023 12:11

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Refactor #161

Refactor #161

gogonzo commented Aug 15, 2023 •

edited

Loading

m7pr commented Aug 23, 2023 •

edited

Loading

gogonzo commented Sep 6, 2023

m7pr commented Sep 6, 2023

averissimo commented Sep 6, 2023 •

edited

Loading

m7pr commented Sep 7, 2023

chlebowa Sep 9, 2023

averissimo Sep 11, 2023

vedhav left a comment •

edited

Loading

chlebowa Sep 11, 2023

chlebowa Sep 11, 2023

chlebowa Sep 11, 2023

gogonzo commented Oct 4, 2023

Refactor #161

Refactor #161

Conversation

gogonzo commented Aug 15, 2023 • edited Loading

install

ddl class

Example connector app

Example teal app with connector

teal app with teal_data

teal.gallery examples

Internal Connectors

What's next

m7pr commented Aug 23, 2023 • edited Loading

gogonzo commented Sep 6, 2023

m7pr commented Sep 6, 2023

averissimo commented Sep 6, 2023 • edited Loading

m7pr commented Sep 7, 2023

chlebowa Sep 9, 2023

Choose a reason for hiding this comment

averissimo Sep 11, 2023

Choose a reason for hiding this comment

vedhav left a comment • edited Loading

Choose a reason for hiding this comment

chlebowa Sep 11, 2023

Choose a reason for hiding this comment

chlebowa Sep 11, 2023

Choose a reason for hiding this comment

chlebowa Sep 11, 2023

Choose a reason for hiding this comment

gogonzo commented Oct 4, 2023

gogonzo commented Aug 15, 2023 •

edited

Loading

m7pr commented Aug 23, 2023 •

edited

Loading

averissimo commented Sep 6, 2023 •

edited

Loading

vedhav left a comment •

edited

Loading