Increase coverage, but also label more interactive parts with nocov

microbiome · Nov 25, 2024 · f2e05cb · f2e05cb
1 parent 87bfa23
commit f2e05cb
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Showing 6 changed files with 37 additions and 15 deletions.
diff --git a/R/landing_page.R b/R/landing_page.R
@@ -19,9 +19,9 @@
 #' @importFrom utils data
 .landing_page <- function(FUN, input, output, session) {
 
+    # nocov start
     mia_datasets <- .import_datasets(-c(2, 5))
 
-    # nocov start
     output$allPanels <- renderUI({
 
         fluidPage(

diff --git a/R/observers.R b/R/observers.R
@@ -338,11 +338,13 @@
 #' @importFrom shiny observeEvent
 .create_launch_observers <- function(FUN, input, session, rObjects) {
 
+    # nocov start
     observeEvent(input$launch, {
 
         .launch_isee(FUN, input$panels, session, rObjects)
 
     }, ignoreInit = TRUE, ignoreNULL = TRUE)
+    # nocov end
 
     invisible(NULL)
 }
diff --git a/R/utils.R b/R/utils.R
@@ -31,21 +31,24 @@
         invokeRestart("muffleMessage")
 
     })
-
+
+    # nocov start
     lapply(messages, showNotification)
+    # nocov end
 
     return(tse)
 }
 
 #' @rdname utils
 #' @importFrom shiny showModal modalDialog
-.print_message <- function(..., title = "Invalid input:"){
+.print_message <- function(..., title = "Invalid input:") {
 
+    # nocov start
     showModal(modalDialog(
         title = title, ...,
         easyClose = TRUE, footer = NULL
     ))
-
+    # nocov end
 }
 
 #' @rdname utils
@@ -64,25 +67,25 @@
 #' @importFrom methods is
 .check_panel <- function(se, panel_list, panel_class, panel_fun, wtext) {
 
-  no_keep <- unlist(lapply(panel_list, function(x) is(x, panel_class)))
+    no_keep <- unlist(lapply(panel_list, function(x) is(x, panel_class)))
 
-  if( any(no_keep) && (is.null(panel_fun(se)) || isEmpty(panel_fun(se))) ){
-    panel_list <- panel_list[!no_keep]
-    warning("no valid ", as.character(substitute(panel_fun)),
+    if( any(no_keep) && (is.null(panel_fun(se)) || isEmpty(panel_fun(se))) ){
+        panel_list <- panel_list[!no_keep]
+        warning("no valid ", as.character(substitute(panel_fun)),
             " fields for ", panel_class, call. = FALSE)
-  }
+    }
 
-  return(panel_list)
+    return(panel_list)
 }
 
 #' @rdname utils
 default_panels <- c("RowDataTable", "ColumnDataTable", "RowTreePlot",
-                    "AbundancePlot", "AbundanceDensityPlot", "ReducedDimensionPlot",
-                    "ComplexHeatmapPlot")
+    "AbundancePlot", "AbundanceDensityPlot", "ReducedDimensionPlot",
+    "ComplexHeatmapPlot")
 
 #' @rdname utils
 other_panels <- c("LoadingPlot", "ColumnTreePlot", "RDAPlot", "ColumnDataPlot",
-                  "RowDataPlot")
+    "RowDataPlot")
 
 #' @rdname utils
 .actionbutton_biocstyle <- "color: #ffffff; background-color: #0092AC; border-color: #2e6da4"
diff --git a/tests/testthat/test-miaDash.R b/tests/testthat/test-miaDash.R
@@ -0,0 +1,5 @@
+test_that("outputs", {
+
+  expect_no_error(miaDash())
+
+})
diff --git a/tests/testthat/test-observers.R b/tests/testthat/test-observers.R
@@ -1,4 +1,4 @@
-test_that(".create_observers works", {
+test_that("observers", {
 
   input <- new.env()
   rObjects <- new.env()

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -4,9 +4,21 @@ test_that("utils", {
     tse <- Tengeler2020
 
     expect_equal(.import_datasets(c(1, 3)), c("GlobalPatterns", "Tengeler2020"))
+
+    expect_no_error(
+        tse <- .update_tse(transformAssay, list(x = tse, assay.type = "counts",
+            method = "relabundance"))
+    )
 
     expect_true(.check_formula("data ~ patient_status + cohort", tse))
     expect_false(.check_formula("data ~ wrong_var + sample_name", tse))
 
-    expect_length(.check_panel(tse, c(RowDataTable()), "RowDataTable", rowData), 1)
+    panels <- c(RowDataTable(), ReducedDimensionPlot())
+
+    expect_warning(
+        expect_length(
+            .check_panel(tse, panels, "ReducedDimensionPlot", reducedDims), 1
+        )
+    )
+
 })