1108 {shinytest2} feature branch (#1126)

Closes #1108 A unified branch for all partial PRs that will solve #1108 Merge at the end. Place where we can unify PRs --------- Signed-off-by: André Veríssimo <[email protected]> Signed-off-by: Marcin <[email protected]> Signed-off-by: Vedha Viyash <[email protected]> Signed-off-by: kartikeya kirar <[email protected]> Co-authored-by: m7pr <[email protected]> Co-authored-by: André Veríssimo <[email protected]> Co-authored-by: Vedha Viyash <[email protected]> Co-authored-by: vedhav <[email protected]> Co-authored-by: kartikeya kirar <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]> Co-authored-by: gogonzo <[email protected]> Co-authored-by: vedhav <[email protected]> Co-authored-by: kartikeyakirar <[email protected]>
insightsengineering · May 10, 2024 · 1cdbc7c · 1cdbc7c
1 parent 340b60b
commit 1cdbc7c
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Showing 41 changed files with 9,720 additions and 9 deletions.
diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -27,6 +27,7 @@ jobs:
     with:
       additional-env-vars: |
         _R_CHECK_CRAN_INCOMING_REMOTE_=false
+        TESTING_DEPTH=5
       additional-r-cmd-check-params: --as-cran
       enforce-note-blocklist: true
       note-blocklist: |

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: teal.modules.clinical
 Title: 'teal' Modules for Standard Clinical Outputs
 Version: 0.9.1.9003
-Date: 2024-05-08
+Date: 2024-05-09
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
     person("Jana", "Stoilova", , "[email protected]", role = "aut"),
@@ -71,6 +71,7 @@ Suggests:
     lubridate (>= 1.7.9),
     nestcolor (>= 0.1.0),
     pkgload,
+    rvest,
     shinytest2,
     styler,
     testthat (>= 3.1.5),
@@ -80,16 +81,16 @@ VignetteBuilder:
 Config/Needs/verdepcheck: insightsengineering/teal,
     insightsengineering/teal.transform, insightsengineering/tern,
     tidymodels/broom, mllg/checkmate, tidyverse/dplyr, rstudio/DT,
-    insightsengineering/formatters, tidyverse/ggplot2, slowkow/ggrepel,
-    r-lib/lifecycle, daroczig/logger, insightsengineering/rlistings,
+    tidyverse/ggplot2, slowkow/ggrepel, r-lib/lifecycle,
+    daroczig/logger, insightsengineering/rlistings,
     rstudio/rmarkdown, insightsengineering/rtables, r-lib/scales,
     rstudio/shiny, daattali/shinyjs, rstudio/shinyvalidate,
     dreamRs/shinyWidgets, insightsengineering/teal.code,
     insightsengineering/teal.data, insightsengineering/teal.logger,
     insightsengineering/teal.reporter, insightsengineering/teal.widgets,
     insightsengineering/tern.gee, insightsengineering/tern.mmrm,
-    tidyverse/tidyr, shosaco/vistime, tidyverse/forcats, yihui/knitr,
-    tidyverse/lubridate, insightsengineering/nestcolor, r-lib/pkgload,
+    shosaco/vistime, tidyverse/forcats, yihui/knitr, tidyverse/lubridate,
+    insightsengineering/nestcolor, r-lib/pkgload, tidyverse/rvest,
     rstudio/shinytest2, r-lib/styler, r-lib/testthat, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3

diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -448,7 +448,7 @@ srv_gee <- function(id,
 
     iv_r <- reactive({
       iv <- shinyvalidate::InputValidator$new()
-      iv$add_rule("conf_level", shinyvalidate::sv_required("Please choose a confidence level."))
+      iv$add_rule("conf_level", shinyvalidate::sv_required("Please choose a confidence level"))
       iv$add_rule(
         "conf_level",
         shinyvalidate::sv_between(

diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
@@ -65,15 +65,14 @@ template_therapy <- function(dataname = "ANL",
 
       dataname[setdiff(cols_to_include, names(dataname))] <- NA
 
-      therapy_table <-
-        dataname %>%
+      therapy_table <- dataname %>%
         dplyr::filter(atirel %in% c("CONCOMITANT", "PRIOR")) %>% # removed PRIOR_CONCOMITANT
         dplyr::select(dplyr::all_of(cols_to_include)) %>%
         dplyr::filter(!is.na(cmdecod)) %>%
         dplyr::mutate(Dosage = paste(cmdose, cmdosu, cmdosfrq, cmroute)) %>%
         dplyr::select(-cmdose, -cmdosu, -cmdosfrq, -cmroute) %>%
         dplyr::select(cmindc, cmdecod, Dosage, dplyr::everything()) %>%
-        dplyr::mutate(CMDECOD = dplyr::case_when(
+        dplyr::mutate(!!cmdecod_char := dplyr::case_when(
           nchar(as.character(cmdecod)) > 20 ~ as.character(cmtrt),
           TRUE ~ as.character(cmdecod)
         )) %>%

diff --git a/tests/testthat/helper-TealAppDriver.R b/tests/testthat/helper-TealAppDriver.R
@@ -23,3 +23,7 @@ init_teal_app_driver <- function(...) {
     .package = "teal"
   )
 }
+
+ns_des_input <- function(id, dataname, type) {
+  sprintf("%s-dataset_%s_singleextract-%s", id, dataname, type)
+}