insightsengineering · gogonzo · Dec 8, 2023 · Nov 23, 2023 · Nov 23, 2023 · Nov 24, 2023
diff --git a/.lintr b/.lintr
@@ -1,6 +1,5 @@
 linters: linters_with_defaults(
-  line_length_linter = line_length_linter(120),
-  cyclocomp_linter = NULL,
-  object_usage_linter = NULL,
-  indentation_linter = NULL
+    line_length_linter = line_length_linter(120),
+    cyclocomp_linter = NULL,
+    object_usage_linter = NULL
   )
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,7 +29,7 @@ Depends:
     goshawk (>= 0.1.15),
     R (>= 3.6),
     shiny,
-    teal (>= 0.14.0.9019)
+    teal (>= 0.14.0.9027)
 Imports:
     checkmate,
     colourpicker,
@@ -44,18 +44,18 @@ Imports:
     shinyjs,
     shinyvalidate,
     stats,
-    teal.code (>= 0.4.0),
+    teal.code (>= 0.4.1.9009),
     teal.logger (>= 0.1.1),
     teal.reporter (>= 0.2.0),
-    teal.transform (>= 0.4.0.9007),
+    teal.transform (>= 0.4.0.9011),
     teal.widgets (>= 0.4.0),
     tidyr
 Suggests:
     knitr,
     nestcolor (>= 0.1.0),
     rmarkdown,
     stringr,
-    teal.data (>= 0.3.0.9010),
+    teal.data (>= 0.3.0.9018),
     tern (>= 0.7.10),
     testthat (>= 2.0),
     utils

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,7 @@
-# teal.goshawk 0.1.15.9002
+# teal.goshawk 0.1.15.9003
+
+### Breaking Changes
+* Adapted all modules to use `teal_data` objects.
 
 ### Enhancements
 

diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R
@@ -327,7 +327,8 @@ srv_g_boxplot <- function(id,
                           hline_vars_labels) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
     # reused in all modules
@@ -531,11 +532,8 @@ srv_g_boxplot <- function(id,
           card$append_text(comment)
         }
         card$append_src(
-          paste(
-            teal.code::get_code(
-              teal.code::join(create_plot(), create_table())
-            ),
-            collapse = "\n"
+          teal.code::get_code(
+            teal.code::join(create_plot(), create_table())
           )
         )
         card

diff --git a/R/tm_g_gh_correlationplot.R b/R/tm_g_gh_correlationplot.R
@@ -378,7 +378,8 @@ srv_g_correlationplot <- function(id,
                                   vline_vars_labels) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
     iv_r <- reactive({
@@ -403,7 +404,7 @@ srv_g_correlationplot <- function(id,
     # filter selected biomarkers
     anl_param <- reactive({
       dataset_var <- dataname
-      ANL <- data[[dataname]]() # nolint
+      ANL <- data()[[dataname]] # nolint
       validate_has_data(ANL, 1)
 
       if (length(input$hline_vars) > 0) {
@@ -492,7 +493,7 @@ srv_g_correlationplot <- function(id,
       )
 
       # analysis
-      private_qenv <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)) %>%
+      private_qenv <- data() %>%
         teal.code::eval_code(
           code = bquote({
             ANL <- .(as.name(dataset_var)) %>% # nolint
@@ -511,7 +512,7 @@ srv_g_correlationplot <- function(id,
       req(constraint_var)
 
       # note that filtered is false thus we cannot use anl_param()$ANL
-      ANL <- data[[dataname]]() # nolint
+      ANL <- data()[[dataname]] # nolint
       validate_has_data(ANL, 1)
 
       validate_has_variable(ANL, param_var)
@@ -525,7 +526,7 @@ srv_g_correlationplot <- function(id,
 
       # get min max values
       if ((constraint_var == "BASE2" && any(grepl("SCR", visit_freq))) ||
-        (constraint_var == "BASE" && any(grepl("BL", visit_freq)))) {
+        (constraint_var == "BASE" && any(grepl("BL", visit_freq)))) { # nolint
         val <- stats::na.omit(switch(constraint_var,
           "BASE" = ANL$BASE[ANL$AVISITCD == "BL"],
           "BASE2" = ANL$BASE2[ANL$AVISITCD == "SCR"],
@@ -841,7 +842,7 @@ srv_g_correlationplot <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(paste(teal.code::get_code(plot_q()), collapse = "\n"))
+        card$append_src(teal.code::get_code(plot_q()))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

diff --git a/R/tm_g_gh_density_distribution_plot.R b/R/tm_g_gh_density_distribution_plot.R
@@ -266,7 +266,8 @@ srv_g_density_distribution_plot <- function(id, # nolint
                                             plot_width) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
     anl_q_output <- constr_anl_q(
@@ -445,11 +446,8 @@ srv_g_density_distribution_plot <- function(id, # nolint
           card$append_text(comment)
         }
         card$append_src(
-          paste(
-            teal.code::get_code(
-              teal.code::join(create_plot(), create_table())
-            ),
-            collapse = "\n"
+          teal.code::get_code(
+            teal.code::join(create_plot(), create_table())
           )
         )
         card

diff --git a/R/tm_g_gh_lineplot.R b/R/tm_g_gh_lineplot.R
@@ -331,7 +331,8 @@ srv_lineplot <- function(id,
                          plot_width) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
     ns <- session$ns
@@ -795,7 +796,7 @@ srv_lineplot <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(paste(teal.code::get_code(plot_q()), collapse = "\n"))
+        card$append_src(teal.code::get_code(plot_q()))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

diff --git a/R/tm_g_gh_scatterplot.R b/R/tm_g_gh_scatterplot.R
@@ -266,7 +266,8 @@ srv_g_scatterplot <- function(id,
                               plot_width) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
     # reused in all modules
@@ -383,7 +384,7 @@ srv_g_scatterplot <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(paste(teal.code::get_code(plot_q()), collapse = "\n"))
+        card$append_src(teal.code::get_code(plot_q()))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

diff --git a/R/tm_g_gh_spaghettiplot.R b/R/tm_g_gh_spaghettiplot.R
@@ -342,7 +342,8 @@ srv_g_spaghettiplot <- function(id,
                                 hline_vars_labels) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
     # reused in all modules
@@ -498,7 +499,7 @@ srv_g_spaghettiplot <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(paste(teal.code::get_code(plot_q()), collapse = "\n"))
+        card$append_src(teal.code::get_code(plot_q()))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

diff --git a/R/utils-arbitrary_lines.r b/R/utils-arbitrary_lines.r
@@ -48,7 +48,6 @@ ui_arbitrary_lines <- function(id, line_arb, line_arb_label, line_arb_color, tit
 #' @keywords internal
 srv_arbitrary_lines <- function(id) {
   moduleServer(id, function(input, output, session) {
-
     comma_sep_to_values <- function(values, wrapper_fun = trimws) {
       vals <- strsplit(values, "\\s{0,},\\s{0,}")[[1]]
       suppressWarnings(wrapper_fun(vals))
@@ -59,8 +58,9 @@ srv_arbitrary_lines <- function(id) {
       iv$add_rule("line_arb", shinyvalidate::sv_optional())
       iv$add_rule(
         "line_arb",
-        ~ if (any(is.na(comma_sep_to_values(., as.numeric))))
+        ~ if (any(is.na(comma_sep_to_values(., as.numeric)))) {
           "Arbitrary lines values should be a comma separated list of numbers"
+        }
       )
 
       iv_color <- shinyvalidate::InputValidator$new()
@@ -69,14 +69,16 @@ srv_arbitrary_lines <- function(id) {
       iv_color$add_rule("line_arb_color", shinyvalidate::sv_optional())
       iv_color$add_rule(
         "line_arb_color",
-        ~ if (!length(comma_sep_to_values(.)) %in% c(1, length(line_arb())))
+        ~ if (!length(comma_sep_to_values(.)) %in% c(1, length(line_arb()))) {
           sprintf(
             "Line input error: number of colors should be equal to 1, the number of lines (%d) or left blank for 'red'",
             length(line_arb())
           )
+        }
       )
-      iv_color$add_rule("line_arb_color", ~ if (!check_color(comma_sep_to_values(.)))
-        "The line colors entered cannot be converted to colors in R, please check your spelling")
+      iv_color$add_rule("line_arb_color", ~ if (!check_color(comma_sep_to_values(.))) {
+        "The line colors entered cannot be converted to colors in R, please check your spelling"
+      })
       iv$add_validator(iv_color)
 
 
@@ -86,11 +88,12 @@ srv_arbitrary_lines <- function(id) {
       iv_label$add_rule("line_arb_label", shinyvalidate::sv_optional())
       iv_label$add_rule(
         "line_arb_label",
-        ~ if (!length(comma_sep_to_values(.)) %in% c(1, length(line_arb())))
+        ~ if (!length(comma_sep_to_values(.)) %in% c(1, length(line_arb()))) {
           sprintf(
             "Line input error: number of labels should be equal to 1, the number of lines (%d) or left blank",
             length(line_arb())
           )
+        }
       )
       iv$add_validator(iv_label)
       iv

diff --git a/R/utils-data_constraints.r b/R/utils-data_constraints.r
@@ -49,6 +49,8 @@ keep_data_const_opts_updated <- function(session, input, data, id_param_var) {
 # param_id: input id that contains values of PARAMCD to filter for
 # param_var: currently only "PARAMCD" is supported
 constr_anl_q <- function(session, input, data, dataname, param_id, param_var, trt_group, min_rows) {
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
   dataset_var <- dataname
   if (!identical(param_var, "PARAMCD")) {
     # why is there a variable param_id which is provided to this function and always equal to "param"?
@@ -60,7 +62,7 @@ constr_anl_q <- function(session, input, data, dataname, param_id, param_var, tr
     validate(need(param_var_value, "Please select a biomarker"))
     checkmate::assert_string(param_var_value)
 
-    ANL <- data[[dataname]]() # nolint
+    ANL <- data()[[dataname]] # nolint
     validate_has_data(ANL, min_rows)
 
     validate_has_variable(ANL, param_var)
@@ -70,7 +72,7 @@ constr_anl_q <- function(session, input, data, dataname, param_id, param_var, tr
     validate_has_variable(ANL, trt_group)
 
     # analysis
-    private_qenv <- teal.code::new_qenv(tdata2env(data), code = teal::get_code_tdata(data)) %>%
+    private_qenv <- data() %>%
       teal.code::eval_code(
         substitute(ANL <- dataname, list(dataname = as.name(dataname))) # nolint
       ) %>%
@@ -91,8 +93,7 @@ constr_anl_q <- function(session, input, data, dataname, param_id, param_var, tr
     constraint_var <- input[["constraint_var"]]
     validate(need(constraint_var, "select a constraint variable"))
 
-
-    ANL <- data[[dataname]]() # nolint
+    ANL <- data()[[dataname]] # nolint
     validate_has_data(ANL, min_rows)
 
     validate_has_variable(ANL, param_var)
@@ -106,7 +107,7 @@ constr_anl_q <- function(session, input, data, dataname, param_id, param_var, tr
 
     # get min max values
     if ((constraint_var == "BASE2" && any(grepl("SCR", visit_freq))) ||
-      (constraint_var == "BASE" && any(grepl("BL", visit_freq)))) {
+      (constraint_var == "BASE" && any(grepl("BL", visit_freq)))) { # nolint
       val <- stats::na.omit(switch(constraint_var,
         "BASE" = ANL$BASE[ANL$AVISITCD == "BL"],
         "BASE2" = ANL$BASE2[ANL$AVISITCD == "SCR"],
@@ -165,21 +166,22 @@ constr_anl_q <- function(session, input, data, dataname, param_id, param_var, tr
 # constraint var means that `param_id.constraint_var` is constrained to the filtered range (or NA),
 # e.g. `ALT.BASE2` (i.e. `PARAMCD = ALT & range_filter_on(BASE2)`)
 create_anl_constraint_reactive <- function(anl_param, input, param_id, min_rows) {
-
   iv_r <- reactive({
     iv <- shinyvalidate::InputValidator$new()
     iv$condition(~ isTRUE(input$constraint_var != "NONE"))
     iv$add_rule("constraint_range_min", shinyvalidate::sv_required("A contraint minimum value is required"))
     iv$add_rule("constraint_range_max", shinyvalidate::sv_required("A contraint maximum value is required"))
     iv$add_rule(
       "constraint_range_min",
-      ~ if (!is.na(input$constraint_range_max) && (.) > input$constraint_range_max)
+      ~ if (!is.na(input$constraint_range_max) && (.) > input$constraint_range_max) {
         "constraint min needs to be less than max"
+      }
     )
     iv$add_rule(
       "constraint_range_max",
-      ~ if (!is.na(input$constraint_range_min) && (.) < input$constraint_range_min)
+      ~ if (!is.na(input$constraint_range_min) && (.) < input$constraint_range_min) {
         "constraint min needs to be less than max"
+      }
     )
     iv
   })
@@ -223,7 +225,7 @@ create_anl_constraint_reactive <- function(anl_param, input, param_id, min_rows)
           ANL <- ANL %>% dplyr::filter(USUBJID %in% filtered_usubjids) # nolint
         })
       )
-     validate_has_data(private_qenv[["ANL"]], min_rows)
+      validate_has_data(private_qenv[["ANL"]], min_rows)
     }
     list(ANL = private_qenv[["ANL"]], qenv = private_qenv)
   })

diff --git a/R/utils.R b/R/utils.R
@@ -38,7 +38,7 @@ plots_per_row_validate_rules <- function(required = TRUE) {
 #' an optional description, and the option to append the filter state list.
 #' Additionally, it display selected constraint options.
 #'
-#' @inheritParams teal.reporter::card_template
+#' @inheritParams teal::report_card_template
 #' @param constraint_list (`list`) a list containing constraint variables, including:
 #'   - constraint_var (`character(1)`) the constraint variable name.
 #'   - constraint_range_min (`numeric(1)`) the minimum constraint range value.

diff --git a/man/report_card_template_goshawk.Rd b/man/report_card_template_goshawk.Rd