chore: make join_key related changes to the modules

insightsengineering · Nov 8, 2023 · 15b6756 · 15b6756
1 parent b5a6470
commit 15b6756
Show file tree

Hide file tree

Showing 38 changed files with 63 additions and 81 deletions.
diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
@@ -31,7 +31,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #' app <- teal::init(
 #'   data = data,
 #'   modules = teal::modules(
@@ -57,7 +57,6 @@
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
 #' }
-#'
 tm_a_pca <- function(label = "Principal Component Analysis",
                      dat,
                      plot_height = c(600, 200, 2000),
@@ -258,7 +257,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
       response[[i]]$select$choices <- var_labels(data[[response[[i]]$dataname]]())
       response[[i]]$select$choices <- setdiff(
         response[[i]]$select$choices,
-        unlist(teal.data::get_join_keys(data)$get(response[[i]]$dataname))
+        unlist(join_keys(data)[[response[[i]]$dataname]])
       )
     }
 
@@ -324,7 +323,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
     anl_merged_input <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = join_keys(data)
     )
 
     anl_merged_q <- reactive({

diff --git a/R/tm_a_regression.R b/R/tm_a_regression.R
@@ -41,7 +41,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = data,
@@ -295,7 +295,7 @@ srv_a_regression <- function(id,
     anl_merged_input <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = join_keys(data)
     )
 
     regression_var <- reactive({

diff --git a/R/tm_data_table.R b/R/tm_data_table.R
@@ -32,7 +32,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = data,

diff --git a/R/tm_front_page.R b/R/tm_front_page.R
@@ -24,7 +24,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' table_1 <- data.frame(Info = c("A", "B"), Text = c("A", "B"))
 #' table_2 <- data.frame(`Column 1` = c("C", "D"), `Column 2` = c(5.5, 6.6), `Column 3` = c("A", "B"))

diff --git a/R/tm_g_association.R b/R/tm_g_association.R
@@ -32,7 +32,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = data,
@@ -251,7 +251,7 @@ srv_tm_g_association <- function(id,
     anl_merged_input <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = join_keys(data)
     )
 
     anl_merged_q <- reactive({

diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
@@ -52,7 +52,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = data,
@@ -441,7 +441,7 @@ srv_g_bivariate <- function(id,
     anl_merged_input <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = join_keys(data)
     )
 
     anl_merged_q <- reactive({

diff --git a/R/tm_g_distribution.R b/R/tm_g_distribution.R
@@ -61,7 +61,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' vars1 <- choices_selected(
 #'   variable_choices(data[["ADSL"]], c("ARM", "COUNTRY", "SEX")),
@@ -447,7 +447,7 @@ srv_distribution <- function(id,
     anl_merged_input <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = join_keys(data)
     )
 
     anl_merged_q <- reactive({

diff --git a/R/tm_g_response.R b/R/tm_g_response.R
@@ -34,7 +34,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = teal.data::cdisc_data(
@@ -278,7 +278,7 @@ srv_g_response <- function(id,
     anl_merged_input <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = join_keys(data)
     )
 
     anl_merged_q <- reactive({

diff --git a/R/tm_g_scatterplot.R b/R/tm_g_scatterplot.R
@@ -44,7 +44,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = data,
@@ -471,7 +471,7 @@ srv_g_scatterplot <- function(id,
     anl_merged_input <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 

diff --git a/R/tm_g_scatterplotmatrix.R b/R/tm_g_scatterplotmatrix.R
@@ -27,7 +27,7 @@
 #' })
 #' datanames <- c("ADSL", "ADRS")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = data,
@@ -180,7 +180,7 @@ srv_g_scatterplotmatrix <- function(id, data, reporter, filter_panel_api, variab
 
     anl_merged_input <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = join_keys(data),
       selector_list = selector_list
     )
 

diff --git a/R/tm_missing_data.R b/R/tm_missing_data.R
@@ -25,7 +25,7 @@
 #' })
 #' datanames <- c("ADSL", "ADRS")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = data,
@@ -356,7 +356,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
   moduleServer(id, function(input, output, session) {
     prev_group_by_var <- reactiveVal("")
     data_r <- data[[dataname]]
-    data_keys <- reactive(teal.data::get_join_keys(data)$get(dataname)[[dataname]])
+    data_keys <- reactive(unlist(join_keys(data)[[dataname]]))
 
     iv_r <- reactive({
       iv <- shinyvalidate::InputValidator$new()
@@ -395,7 +395,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
 
     data_parent_keys <- reactive({
       if (length(parent_dataname) > 0 && parent_dataname %in% names(data)) {
-        keys <- teal.data::get_join_keys(data)$get(dataname)
+        keys <- teal.data::join_keys(data)[[dataname]]
         if (parent_dataname %in% names(keys)) {
           keys[[parent_dataname]]
         } else {

diff --git a/R/tm_outliers.R b/R/tm_outliers.R
@@ -23,7 +23,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' fact_vars_adsl <- names(Filter(isTRUE, sapply(data[["ADSL"]], is.factor)))
 #' vars <- choices_selected(variable_choices(data[["ADSL"]], fact_vars_adsl))
@@ -66,7 +66,6 @@
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
 #' }
-#'
 tm_outliers <- function(label = "Outliers Module",
                         outlier_var,
                         categorical_var = NULL,
@@ -294,7 +293,7 @@ srv_outliers <- function(id, data, reporter, filter_panel_api, outlier_var,
     anl_merged_input <- teal.transform::merge_expression_srv(
       selector_list = reactive_select_input,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
@@ -477,7 +476,7 @@ srv_outliers <- function(id, data, reporter, filter_panel_api, outlier_var,
           },
           env = list(
             dataname = as.name(dataname_first),
-            join_keys = as.character(teal.data::get_join_keys(data)$get(dataname_first)[[dataname_first]])
+            join_keys = as.character(join_keys(data)[[dataname_first]][[dataname_first]])
           )
         )
       )

diff --git a/R/tm_t_crosstable.R b/R/tm_t_crosstable.R
@@ -29,7 +29,7 @@
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = teal.data::cdisc_data(
@@ -75,7 +75,6 @@
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
 #' }
-#'
 tm_t_crosstable <- function(label = "Cross Table",
                             x,
                             y,
@@ -219,7 +218,7 @@ srv_t_crosstable <- function(id, data, reporter, filter_panel_api, label, x, y,
 
     anl_merged_input <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = join_keys(data),
       selector_list = selector_list,
       merge_function = merge_function
     )

diff --git a/R/tm_variable_browser.R b/R/tm_variable_browser.R
@@ -38,7 +38,7 @@
 #' })
 #' datanames <- c("ADSL", "ADTTE")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- teal::init(
 #'   data = data,
@@ -1149,9 +1149,9 @@ render_tab_header <- function(dataset_name, output, data) {
   dataset_ui_id <- paste0("dataset_summary_", dataset_name)
   output[[dataset_ui_id]] <- renderText({
     df <- data[[dataset_name]]()
-    join_keys <- teal.data::get_join_keys(data)
+    join_keys <- join_keys(data)
     if (!is.null(join_keys)) {
-      key <- teal.data::get_join_keys(data)$get(dataset_name)[[dataset_name]]
+      key <- join_keys(data)[[dataset_name]][[dataset_name]]
     } else {
       key <- NULL
     }
@@ -1222,9 +1222,9 @@ render_tab_table <- function(dataset_name, parent_dataname, output, data, input,
       # get icons proper for the data types
       icons <- stats::setNames(teal.slice:::variable_types(df), colnames(df))
 
-      join_keys <- teal.data::get_join_keys(data)
+      join_keys <- join_keys(data)
       if (!is.null(join_keys)) {
-        icons[intersect(join_keys$get(dataset_name)[[dataset_name]], colnames(df))] <- "primary_key"
+        icons[intersect(join_keys[[dataset_name]][[dataset_name]], colnames(df))] <- "primary_key"
       }
       icons <- variable_type_icons(icons)
 

diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd
diff --git a/man/tm_a_regression.Rd b/man/tm_a_regression.Rd
diff --git a/man/tm_data_table.Rd b/man/tm_data_table.Rd
diff --git a/man/tm_front_page.Rd b/man/tm_front_page.Rd
diff --git a/man/tm_g_association.Rd b/man/tm_g_association.Rd
diff --git a/man/tm_g_bivariate.Rd b/man/tm_g_bivariate.Rd
diff --git a/man/tm_g_distribution.Rd b/man/tm_g_distribution.Rd
diff --git a/man/tm_g_response.Rd b/man/tm_g_response.Rd
diff --git a/man/tm_g_scatterplot.Rd b/man/tm_g_scatterplot.Rd
diff --git a/man/tm_g_scatterplotmatrix.Rd b/man/tm_g_scatterplotmatrix.Rd