[Bug]: Code on the teal_data is omitted

[llrs-roche]

What happened?

For insightsengineering/teal.modules.clinical#1437 I found that some expressions are missed on teal:

data <- within(teal_data(), {
  ADSL <- teal.modules.clinical::tmc_ex_adsl
  ADSL$SEX[sample(seq_len(nrow(ADSL)), 50)] <- NA
})

app <- init(
  data = data,
  modules = example_module()
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

The last line is missing from the app:

But it is present on the qenv.

data |> get_code() |> cat()
# ADSL <- teal.modules.clinical::tmc_ex_adsl
# ADSL$SEX[sample(seq_len(nrow(ADSL)), 50)] <- NA

A more minimal reprex is below:

data <- within(teal.code::qenv(), {
  iris <- iris
  iris$Species[sample(seq_len(nrow(iris)), 50)] <- NA
})
teal.code::get_code(data, names = "iris") |> cat()
#> iris <- iris

See diagnostics on comments below but it seems $<- and [<- is not picked by get_code

sessionInfo()

Relevant log output

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[averissimo]

The last line is not recognized as ADSL by teal.code, here's a smaller snippet

data <- within(teal.code::qenv(), {
  iris <- iris
  iris$Species[sample(seq_len(nrow(iris)), 50)] <- NA
})
teal.code::get_code(data, names = "iris") |> cat()
#> iris <- iris

[m7pr]

Looks like teal.code::get_code records top-level bindings (e.g., <- to iris), but it does not track in-place mutations via subassignment ($<-, [<-).

We either add a line # @linksto ADSL or we do a fix in teal.code

[m7pr]

@llrs-roche by the way

you can write

sample.int(nrow(iris), 50)

instead of

sample(seq_len(nrow(ADSL)), 50)

[averissimo]

Looks like teal.code::get_code records top-level bindings (e.g., <- to iris), but it does not track in-place mutations via subassignment ($<-, [<-).

We either add a line # @linksto ADSL or we do a fix in teal.code

This kind of code seems plausible to encounter. I'd vote to fix in teal.code

[averissimo]

This works though:

teal.data::teal_data() |> within({ 
  ADSL <- teal.data::rADSL
  ADSL$Yada <- 1
}) |> teal.code::get_code(names = "ADSL") |> cat()
#> ADSL <- teal.data::rADSL
#> ADSL$Yada <- 1

[llrs-roche]

I agree with @averissimo, this should be fixed on teal.code. Moving issue there and updating the top level message with the more minimal example.

[m7pr]

I think its the combination of $ and [ on LHS. Working on it now locally

[llrs-roche]

The left to right assignment also fails:

data <- within(teal.code::qenv(), {
  iris <- iris
  NA -> iris$Species[sample(seq_len(nrow(iris)), 50)]
  iris
})
teal.code::get_code(data, names = "iris") |> cat()
## iris <- iris

[m7pr]

$ and [ doesnt work

> teal.data::teal_data() |> within({ 
+   ADSL <- teal.data::rADSL
+   ADSL$Yada[ADSL$AGE > 30] <- 1
+ }) |> teal.code::get_code(names = "ADSL") |> cat()
ADSL <- teal.data::rADSL

When split to 2 lines it works

> teal.data::teal_data() |> within({ 
+   ADSL <- teal.data::rADSL
+   ind <- ADSL$AGE > 30
+   ADSL$Yada[ind] <- 1
+ }) |> teal.code::get_code(names = "ADSL") |> cat()
ADSL <- teal.data::rADSL
ind <- ADSL$AGE > 30
ADSL$Yada[ind] <- 1

So maybe it's the case of ADSL$*[ADSL*]