[Bug]: `get_code` does not retrieve code in some cases

[chlebowa]

What happened?

Code retrieval fails if code passed as character but not if passed as language.

1. Create language obejct and evaluate to create data in global environment.

library(teal)

code <- bquote({
  ADSL <- teal.modules.clinical::tmc_ex_adsl
  ADRS <- teal.modules.clinical::tmc_ex_adrs |>
    dplyr::mutate(
      AVALC = tern::d_onco_rsp_label(AVALC) |>
        formatters::with_label("Character Result/Finding")
    ) |>
    dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
})
eval(code)

2. Create teal_data by passing code as is.

Code retrieved correctly.

data1 <- teal.data::cdisc_data(
  ADRS = ADRS,
  ADSL = ADSL,
  code = code
)
teal.data::get_code(data, dataname = "ADRS")

[1] "warning('Code was not verified for reproducibility.')\nADRS <- dplyr::filter(dplyr::mutate(teal.modules.clinical::tmc_ex_adrs, AVALC = formatters::with_label(tern::d_onco_rsp_label(AVALC), \"Character Result/Finding\")), PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")"

3. Create teal_data by passing code as character.

Code retrieved fails.

data2 <- teal.data::cdisc_data(
  ADRS = ADRS,
  ADSL = ADSL,
  code = code |> deparse()
)
teal.data::get_code(data, dataname = "ADRS")

[1] "warning('Code was not verified for reproducibility.')"
Warning message:
In sym_cond > ass_cond :
  longer object length is not a multiple of shorter object length

This only occurs with datanames specified.

sessionInfo()

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: Europe/Warsaw
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] teal_0.15.2      teal.slice_0.5.1 teal.data_0.6.0  teal.code_0.5.0
[5] shiny_1.8.1.1

loaded via a namespace (and not attached):
 [1] sandwich_3.1-0              utf8_1.2.4
 [3] generics_0.1.3              tidyr_1.3.1
 [5] tern.gee_0.1.3              lattice_0.22-5
 [7] digest_0.6.35               magrittr_2.0.3
 [9] estimability_1.5            grid_4.3.3
[11] mvtnorm_1.2-4               fastmap_1.1.1
[13] Matrix_1.6-5                backports_1.4.1
[15] survival_3.5-8              multcomp_1.4-25
[17] promises_1.3.0              purrr_1.0.2
[19] fansi_1.0.6                 scales_1.3.0
[21] TH.data_1.1-2               codetools_0.2-19
[23] Rdpack_2.6                  cli_3.6.2
[25] teal.transform_0.5.0        rlang_1.1.3
[27] rbibutils_2.2.16            splines_4.3.3
[29] munsell_0.5.1               geepack_1.3.10
[31] tools_4.3.3                 checkmate_2.3.1
[33] teal.modules.clinical_0.9.1 dplyr_1.1.4
[35] colorspace_2.1-0            ggplot2_3.5.0
[37] httpuv_1.6.15               formatters_0.5.6
[39] broom_1.0.5                 rtables_0.6.7
[41] vctrs_0.6.5                 logger_0.3.0
[43] R6_2.5.1                    mime_0.12
[45] zoo_1.8-12                  emmeans_1.10.1
[47] lifecycle_1.0.4             MASS_7.3-60.0.1
[49] pkgconfig_2.0.3             teal.logger_0.2.0
[51] pillar_1.9.0                later_1.3.2
[53] gtable_0.3.4                glue_1.7.0
[55] Rcpp_1.0.12                 tibble_3.2.1
[57] tidyselect_1.2.1            xtable_1.8-4
[59] nlme_3.1-164                htmltools_0.5.8.1
[61] compiler_4.3.3              tern_0.9.4

Relevant log output

No response

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[chlebowa]

Oddly, this works just fine:

ADSL <- teal.modules.clinical::tmc_ex_adsl
ADRS <- teal.modules.clinical::tmc_ex_adrs |>
  dplyr::mutate(
    AVALC = tern::d_onco_rsp_label(AVALC) |>
      formatters::with_label("Character Result/Finding")
  ) |>
  dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")

code <- '
  ADSL <- teal.modules.clinical::tmc_ex_adsl
  ADRS <- teal.modules.clinical::tmc_ex_adrs |>
    dplyr::mutate(
      AVALC = tern::d_onco_rsp_label(AVALC) |>
        formatters::with_label("Character Result/Finding")
    ) |>
    dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
'
data3 <- teal.data::cdisc_data(
  ADRS = ADRS,
  ADSL = ADSL,
  code = code
)
teal.data::get_code(data3, dataname = "ADRS")

[1] "warning('Code was not verified for reproducibility.')\nADRS <- dplyr::filter(dplyr::mutate(teal.modules.clinical::tmc_ex_adrs, AVALC = formatters::with_label(tern::d_onco_rsp_label(AVALC), \"Character Result/Finding\")), PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")"

[m7pr]

@chlebowa thanks for pointing that.

It actually works for

code <- '
  ADSL <- teal.modules.clinical::tmc_ex_adsl
  ADRS <- teal.modules.clinical::tmc_ex_adrs |>
    dplyr::mutate(
      AVALC = tern::d_onco_rsp_label(AVALC) |>
        formatters::with_label("Character Result/Finding")
    ) |>
    dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
'
teal.data::get_code(teal_data(ADRS = ADRS, ADSL = ADSL, code = code), dataname = "ADRS")

and fails for

code2 <- 
'{     
  ADSL <- teal.modules.clinical::tmc_ex_adsl
  ADRS <- teal.modules.clinical::tmc_ex_adrs |>
    dplyr::mutate(
      AVALC = tern::d_onco_rsp_label(AVALC) |>
        formatters::with_label("Character Result/Finding")
    ) |>
    dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
}'
teal.data::get_code(teal_data(ADRS = ADRS, ADSL = ADSL, code = code2), dataname = "ADRS")

where the only difference is that the second case has {} at the beginning and at the end. This is also the case with code |> deparse() that adds those parenthesis around the code. I think we should investigate and improve the parser so that it removes {} curly brackets before it parses the code

[m7pr]

Provided a fix for this in https://github.com/insightsengineering/teal.data/pull/311