qenv warnings (#181)

Signed-off-by: Dawid Kałędkowski <6959016+gogonzo@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Blazewim <marek.blazewicz@contractors.roche.com> Co-authored-by: Nikolas Burkoff <nikolas.burkoff@roche.com> Co-authored-by: Dawid Kałędkowski <dawid.kaledkowski@gmail.com> Co-authored-by: Dawid Kałędkowski <6959016+gogonzo@users.noreply.github.com>
insightsengineering · Oct 27, 2022 · 7c0dba8 · 7c0dba8
1 parent f49ca0f
commit 7c0dba8
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Showing 9 changed files with 114 additions and 24 deletions.
diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R
@@ -209,7 +209,10 @@ ui_g_ae_oview <- function(id, ...) {
         footnotes = ""
       )
     ),
-    forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+    forms = tagList(
+      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+    )
   )
 }
 
@@ -294,13 +297,12 @@ srv_g_ae_oview <- function(id,
         input$arm_trt,
         message_fmt = "Must not be equal to Treatment"
       ))
-
       iv_comp$enable()
-      validate(need(iv_comp$is_valid(), "Misspecification error: please observe red flags in the encodings."))
 
+      validate(need(iv_comp$is_valid(), "Misspecification error: please observe red flags in the encodings."))
       validate(need(nlevels(ANL[[input$arm_var]]) > 1, "Arm needs to have at least 2 levels"))
       validate_has_data(ANL, min_nrow = 10)
-      if (all(c(input$arm_trt, input$arm_ref) %in% ANL_UNFILTERED[[input$arm_var]])) {
+      if (all(c(input$arm_trt, input$arm_ref) %in% ANL[[input$arm_var]])) {
         iv_an <- shinyvalidate::InputValidator$new()
         iv_an$add_rule("arm_ref", shinyvalidate::sv_in_set(set = ANL[[input$arm_var]]))
         iv_an$add_rule("arm_trt", shinyvalidate::sv_in_set(set = ANL[[input$arm_var]]))
@@ -310,7 +312,7 @@ srv_g_ae_oview <- function(id,
       validate(need(all(c(input$arm_trt, input$arm_ref) %in% unique(ANL[[input$arm_var]])), "Plot loading"))
 
       q1 <- teal.code::eval_code(
-        teal.code::new_qenv(tdata2env(data), code = get_code(data)),
+        teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
         code = as.expression(c(
           bquote(anl_labels <- formatters::var_labels(.(as.name(dataname)), fill = FALSE)),
           bquote(flags <- .(as.name(dataname)) %>%
@@ -344,6 +346,13 @@ srv_g_ae_oview <- function(id,
 
     plot_r <- reactive(output_q()[["plot"]])
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

diff --git a/R/tm_g_ae_sub.R b/R/tm_g_ae_sub.R
@@ -161,7 +161,10 @@ ui_g_ae_sub <- function(id, ...) {
         )
       )
     ),
-    forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+    forms = tagList(
+      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+    )
   )
 }
 
@@ -336,7 +339,7 @@ srv_g_ae_sub <- function(id,
         bquote(group_labels <- setNames(.(group_labels), .(input$groups)))
       }
 
-      q1 <- teal.code::eval_code(teal.code::new_qenv(tdata2env(data), code = get_code(data)), code = group_labels_call)
+      q1 <- teal.code::eval_code(teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)), code = group_labels_call)
       q2 <- teal.code::eval_code(q1, code = "")
       teal.code::eval_code(
         q2,
@@ -365,6 +368,13 @@ srv_g_ae_sub <- function(id,
 
     plot_r <- reactive(output_q()[["plot"]])
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       verbatim_content = reactive(teal.code::get_code(output_q())),

diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R
@@ -252,7 +252,10 @@ ui_g_butterfly <- function(id, ...) {
         value = a$legend_on
       )
     ),
-    forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
+    forms = tagList(
+      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+    ),
     pre_output = a$pre_output,
     post_output = a$post_output
   )
@@ -407,7 +410,7 @@ srv_g_butterfly <- function(id, data, filter_panel_api, reporter, dataname, labe
       anl_vars <- unique(c("USUBJID", "STUDYID", varlist_from_anl)) # nolint
 
       q1 <- teal.code::eval_code(
-        teal.code::new_qenv(tdata2env(data), code = get_code(data)),
+        teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
         code = bquote({
           ADSL <- ADSL[, .(adsl_vars)] %>% as.data.frame() # nolint
           ANL <- .(as.name(dataname))[, .(anl_vars)] %>% as.data.frame() # nolint
@@ -489,6 +492,13 @@ srv_g_butterfly <- function(id, data, filter_panel_api, reporter, dataname, labe
       width = plot_width
     )
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       title = paste("R code for", label),

diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R
@@ -190,7 +190,10 @@ ui_g_events_term_id <- function(id, ...) {
         footnotes = ""
       )
     ),
-    forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+    forms = tagList(
+      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+    )
   )
 }
 
@@ -315,7 +318,7 @@ srv_g_events_term_id <- function(id,
       anl_vars <- c("USUBJID", "STUDYID", input$term) # nolint
 
       q1 <- teal.code::eval_code(
-        teal.code::new_qenv(tdata2env(data), code = get_code(data)),
+        teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
         code = bquote(
           ANL <- merge( # nolint
             x = ADSL[, .(adsl_vars), drop = FALSE],
@@ -357,6 +360,13 @@ srv_g_events_term_id <- function(id,
 
     plot_r <- reactive(output_q()[["plot"]])
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       title = paste("R code for", label),

diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R
@@ -288,7 +288,10 @@ ui_g_heatmap_bygrade <- function(id, ...) {
           footnotes = ""
         )
       ),
-      forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+      forms = tagList(
+        teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+        teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+      )
     )
   )
 }
@@ -377,7 +380,7 @@ srv_g_heatmap_bygrade <- function(id,
         paste("Please de-select", input$id_var, "in annotation variable(s)", sep = " ")
       ))
 
-      if (input$plot_cm) {
+      if (isTRUE(input$plot_cm)) {
         ADCM <- data[[cm_dataname]]() # nolint
         validate(
           need(
@@ -395,15 +398,15 @@ srv_g_heatmap_bygrade <- function(id,
         ))
       }
 
-      q1 <- if (input$plot_cm) {
+      q1 <- if (isTRUE(input$plot_cm)) {
         iv_cm <- shinyvalidate::InputValidator$new()
         conmed_var <- input$conmed_var
         iv_cm$add_rule("conmed_var", shinyvalidate::sv_required())
         iv_cm$enable()
         validate(need(iv_cm$is_valid(), "Misspecification error: please observe red flags in the encodings."))
 
         teal.code::eval_code(
-          teal.code::new_qenv(tdata2env(data), code = get_code(data)),
+          teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
           code = bquote({
             conmed_data <- ADCM %>%
               filter(!!sym(.(conmed_var)) %in% .(input$conmed_level))
@@ -447,6 +450,13 @@ srv_g_heatmap_bygrade <- function(id,
 
     plot_r <- reactive(output_q()[["plot"]])
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       title = paste("R code for", label),

diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R
@@ -394,7 +394,10 @@ ui_g_patient_profile <- function(id, ...) {
           value = a$x_limit
         )
       ),
-      forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
+      forms = tagList(
+        teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+        teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+      ),
       pre_output = a$pre_output,
       post_output = a$post_output
     )
@@ -632,9 +635,10 @@ srv_g_patient_profile <- function(id,
         lb_dataname
       )
       input_select <- purrr::map_lgl(datanames, is.na)
+
       select_plot <- purrr::map2_lgl(
         input_select, possible_plot,
-        ~ if (!.x) {
+        ~ if (!.x && paste("select", .y, sep = "_") %in% names(input)) {
           input[[paste("select", .y, sep = "_")]]
         } else {
           FALSE
@@ -650,7 +654,7 @@ srv_g_patient_profile <- function(id,
       empty_lb <- FALSE
 
       q1 <- teal.code::eval_code(
-        teal.code::new_qenv(tdata2env(data), code = get_code(data)),
+        teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
         code = bquote({
           ADSL <- ADSL %>% # nolint
             group_by(.data$USUBJID)
@@ -1068,6 +1072,13 @@ srv_g_patient_profile <- function(id,
       width = plot_width
     )
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       title = paste("R code for", label),

diff --git a/R/tm_g_spiderplot.R b/R/tm_g_spiderplot.R
@@ -209,7 +209,10 @@ ui_g_spider <- function(id, ...) {
           value = a$href_line
         )
       ),
-      forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
+      forms = tagList(
+        teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+        teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+      ),
       pre_output = a$pre_output,
       post_output = a$post_output
     )
@@ -271,7 +274,7 @@ srv_g_spider <- function(id, data, filter_panel_api, reporter, dataname, label,
 
       # merge
       q1 <- teal.code::eval_code(
-        teal.code::new_qenv(tdata2env(data), code = get_code(data)),
+        teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
         code = bquote({
           ADSL <- ADSL[, .(adsl_vars)] %>% as.data.frame() # nolint
           ADTR <- .(as.name(dataname))[, .(adtr_vars)] %>% as.data.frame() # nolint
@@ -379,6 +382,13 @@ srv_g_spider <- function(id, data, filter_panel_api, reporter, dataname, label,
       width = plot_width
     )
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       title = paste("R code for", label),

diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R
@@ -243,7 +243,10 @@ ui_g_swimlane <- function(id, ...) {
           value = paste(a$vref_line, collapse = ", ")
         )
       ),
-      forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
+      forms = tagList(
+        teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+        teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+      ),
       pre_output = a$pre_output,
       post_output = a$post_output
     )
@@ -316,7 +319,7 @@ srv_g_swimlane <- function(id,
 
       ADSL <- data[["ADSL"]]() # nolint
 
-      q1 <- teal.code::new_qenv(tdata2env(data), code = get_code(data))
+      q1 <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))
 
       # VARIABLE GETTERS
       # lookup bar variables
@@ -513,6 +516,13 @@ srv_g_swimlane <- function(id,
       width = plot_width
     )
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
       title = paste("R code for", label),

diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R
@@ -265,7 +265,10 @@ ui_g_waterfall <- function(id, ...) {
         value = a$gap_point_val
       )
     ),
-    forms = teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code"),
+    forms = tagList(
+      teal.widgets::verbatim_popup_ui(ns("warning"), "Show Warnings"),
+      teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+    ),
     pre_output = a$pre_output,
     post_output = a$post_output
   )
@@ -388,7 +391,7 @@ srv_g_waterfall <- function(id,
 
       # write variables to qenv
       q1 <- teal.code::eval_code(
-        teal.code::new_qenv(tdata2env(data), code = get_code(data)),
+        teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
         code = bquote({
           bar_var <- .(bar_var)
           bar_color_var <- .(bar_color_var)
@@ -521,6 +524,13 @@ srv_g_waterfall <- function(id,
       width = plot_width
     )
 
+    teal.widgets::verbatim_popup_srv(
+      id = "warning",
+      verbatim_content = reactive(teal.code::get_warnings(output_q())),
+      title = "Warning",
+      disabled = reactive(is.null(teal.code::get_warnings(output_q())))
+    )
+
     # Show R Code
     teal.widgets::verbatim_popup_srv(
       id = "rcode",